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Migrants in Hungary, near the border with Serbia, were taken to a camp early on Thursday.Credit Dan Kitwood/Getty Images

BUDAPEST — Rain, misery and more confusion marked the continuing trek of migrants from Syria and other Middle Eastern nations across Europe on Thursday, as thousands endured a drenching downpour, the threat of resistance and changes in their ability to cross borders.

The asylum seekers were coping with conflicting messages from Europe, ranging from warm welcomes in some places to a series of new constraints on their ability to get where they want to go: Hungary mobilized its army on its border with Serbia as a prelude to an increased role for the military in its response; Austria halted its rail service across the border with Hungary under the strain of the migration influx; and a leading far-right politician in the Netherlands warned of an “Islamic invasion.”

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The sometimes-wrenching changes from day to day only underscored the lack of unity throughout Europe, the day after a top European Union official called for the member nations to put aside their differences and commit to a series of unified responses to Europe’s worst humanitarian crisis in decades.

Graphic The Scale of the Migrant Crisis, From 160 to Millions The latest E.U. proposal addresses just a fraction of a human crisis numbering in the millions. OPEN Graphic

At least 7,000 migrants, including parents with small children, passed the border between Greece and Macedonia on Thursday, confronting heavy rainfall, muddy roads and immense piles of garbage as Macedonia, a poor Balkan country and a candidate to join the European Union, announced that it might follow Hungary’s example and build a fence to keep migrants out.

Jasmin Redzepi, president of Legis, an organization that has been helping migrants and refugees passing through the country, said the situation was “very serious” since the capacity of tents to house refugees at the main registration center near the border was limited to about 700 people.

Denmark, which had temporarily closed a highway running north from the German border to try to contain migrants seeking to travel to Sweden and other countries, said on Thursday that it would not impede their progress. The about-face highlighted confusion over how to apply European Union rules, which require migrants to register or seek asylum in the country of their arrival. Denmark has recently lowered benefits it gives to migrants, and many of those traveling through the country do not want to remain there.

Among the toughest responses to the crisis has been in Hungary, where the army on Thursday was conducting exercises near the border with Serbia, a possible prelude to a more active role as thousands continued to pour into the country overnight.

The involvement of the army in policing the border, where a 110-mile fence with razor wire is being constructed to keep migrants out, is subject to the approval of a bill in Parliament this month.

The number of migrants in the area has shown no sign of abating, and Hungarian military officials have said the army would help secure the country’s borders.

Graphic Seeking a Fair Distribution of Migrants in Europe German and European Union leaders have called for European countries to share the burden of absorbing the hundreds of thousands of migrants who have poured into the continent this summer. OPEN Graphic

More than 3,000 migrants crossed the border into Austria from Hungary overnight, and another 3,000 or so were expected to arrive in the area on Thursday, the police and Red Cross officials at the border said. Rail service was halted between the two countries on Thursday, Reuters reported, because Austria could not handle the huge number of migrants crossing the border. It was not clear when service would resume.

The Hungarian police detained 3,321 people for crossing the border illegally on Wednesday, the highest daily figure so far this year, according to data published by the police.

Jean-Claude Juncker, the president of the European Commission, the executive arm of the European Union, on Wednesday issued an impassioned call for countries across the 28-nation bloc to overcome divisions, and invoked Europe’s historical imperative not to turn its back on the huge number of migrants streaming in.

Mr. Juncker proposed that the European Union accept and distribute 160,000 migrants across its member nations, and he implored Europeans not to forget their ancestors who had also fled hardship, poverty and famine.

Mr. Juncker’s plea appeared to have been embraced by Prime Minister Ewa Kopacz of Poland, who was quoted by Reuters as saying that she had heard and understood his message. Responding to comments by the opposition that Poland should not heed the European Union’s calls, she said, “Calls for Polish solidarity is no blackmail.”

“Acting jointly and efficiently in the E.U. is in our interest,” she said. “Let’s be decent. President Juncker has reminded us that once, we were also refugees.”

But in Germany, where Chancellor Angela Merkel has been pushing for mandatory quotas, even some supporters of the quotas acknowledged that they were unlikely to be accepted across the bloc.

Mr. Juncker’s “latest plan is definitely a move in the right direction,” the left-leaning newspaper Süddeutsche Zeitung said in an editorial on Thursday. “He will surely know, however, that the plan is very unlikely to be implemented. The resistance of individual countries may take it apart — and with it the entire European project.”

Such resistance was evident in Hungary, where Janos Lazar, the prime minister’s chief of staff, reiterated the country’s rejection of a quota system. “The government won’t accept the diktat, which several European powers are trying to force onto Hungary,” he said.

In Netherlands, the far-right politician Geert Wilders was even more emphatic, calling the influx of migrants to Europe an “Islamic invasion” in a parliamentary debate on Thursday, Reuters reported, and underlining that country’s struggle over how to respond to the crisis.

“Masses of young men in their 20s with beards singing ‘Allahu akbar’ across Europe. It’s an invasion that threatens our prosperity, our security, our culture and identity,” he was quoted as saying by the news agency.

The Dutch government has indicated a willingness to accept more migrants if the quota system is embraced across the bloc. But, as in many European countries, there has been a fierce debate in the Netherlands about the challenges of immigration, and Mr. Wilders and his Party for Freedom have been citing the crisis to argue that the country risks being overcome by Muslim migrants who do not subscribe to the Netherlands’ vaunted liberal values.

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Advocates for migrants argued that the commission’s proposals, however well intentioned, were insufficient to address a growing challenge. The plan amounted to small steps to protect migrants, Iverna McGowan, the acting director of the European Institutions Office at Amnesty International, said on Wednesday, adding that more resources were needed to handle the influx in a humane way.

Ms. McGowan suggested that the commission was misguided in focusing its resources on returning migrants to so-called safe countries — nations like Albania, Serbia and Turkey that it says are free of persecution, torture, inhuman or degrading treatment or punishment, indiscriminate violence and armed conflict. Such a policy might result in people who would otherwise qualify for asylum being sent back to persecution, she said.

“Member states should be looking to increase safe routes into the E.U.,” she said, “not safe countries to send them back to.”

Austria and Germany threw open their borders over the weekend, in what was described as a one-time gesture for migrants. But so far, there has been no attempt to halt the flow of arrivals. Almost all the migrants who have come from Hungary in recent days opt to continue on to Germany rather than apply for asylum in Austria.

But a backlash is brewing among far-right anti-immigrant groups in Germany, and it remains unclear how far that country’s capacity can be stretched. Germany expects more than 800,000 asylum seekers to arrive in the country this year, and more than half that number are already in the country, according to Sigmar Gabriel, the country’s vice chancellor.

“Germany registered 450,000 refugees, including 105,000 in August and 73,000 in the first eight days of September,” Mr. Gabriel told Parliament in Berlin. “There may be more than 100,000 in September.”

More than 200 people spent the night in Flensburg, Germany, the last station before the border with Denmark, officials there said. Humanitarian organizations brought food and water and organized buses to bring many of them to a shelter where they could spend the night before continuing their journey on Thursday, the police said.

Many of those seeking to reach Finland, Norway and Sweden were expected to catch buses to the port city of Kiel in northern Germany on Thursday, said Mandy Lorenzen a spokeswoman for the police in Flensburg. From there, they could take ferries to Sweden.

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