At least 13 migrants, including children, have died after their dinghy and a ferry collided off Turkey, the coastguard there says.
The accident happened close to the port of Canakkale. The boat was on its way to the Greek island of Lesbos.
In a second incident, Greece's coastguard said 26 people were feared missing from a boat, also off Lesbos.
Meanwhile thousands of migrants continue to cross borders in southern Europe, many now passing into Austria.
'We lost the children'
Turkey's coastguard said it had raised the alarm after being told that a commercial vessel and a migrant boat had collided off Canakkale.
It said it had sent a helicopter and six rescue boats to the area.
Eight people have been rescued, with one seriously injured. Some reports said four of the dead were children.
One survivor who gave his name as Haseen, told AFP news agency: "It was dark, we saw the ship bearing down on us. We tried to signal with flashlights and cell phones but they did not see us."
The passengers were thrown into the water.
"We lost the children. We could not see them in the dark," Haseen said.
In the second incident, Greece's coastguard said it had rescued 22 people spotted in the water near Lesbos — but a further 26 people were feared missing.
On Saturday, a five-year-old girl died and 13 people were feared missing after their boat also sank off Lesbos.
Trips on makeshift craft between Turkey and Greek islands are frequent and dangerous for migrants, many of whom are fleeing conflict in Iraq, Syria and Afghanistan.
Meanwhile, thousands of migrants continue to cross borders further north, many of them hoping to reach Germany and Scandinavia.
Austria saw the arrival of at least 10,000 migrants on Saturday and 7,000 more are now crowding the Nickelsdorf crossing with Hungary.
Germany says it now expects two trains from Austria, carrying 1,000 migrants in total, to cross its border at Freilassing on Sunday evening.
Five more trains, carrying 500 each, are expected on Monday. German police said a planned centre for 400 migrants in Wertheim in southern Germany was destroyed in an arson attack on Sunday morning.
Long queues of both people and traffic have been reported at Slovenia's borders with Croatia and Austria amid tighter restrictions.
Austria, Hungary, Slovenia and Croatia have all traded accusations of failure to deal effectively with the crisis over the past few days.
Croatia initially welcomed the migrants but then said it was unable to cope with the numbers and moved them over the border to Hungary, which quickly ferried them on to Austria.
Hungary and Romania have now also criticised each other over Hungary's plans to build a fence along their border. Hungary has already completed a razor-wire fence along its Serbian frontier and is building one on its Croatian border.
Romanian Foreign Minister Bogdan Aurescu called Hungary's actions "autistic and unacceptable".
Hungarian Foreign Minister Peter Szijjarto said he expected "more modesty from a foreign minister whose prime minister is currently facing trial", referring to an ongoing corruption case.
The EU has been strongly criticised for its failure to co-ordinate a response to the migrant crisis.
Interior ministers will hold an emergency meeting on Tuesday in another attempt to agree on relocating migrants with binding quotas for each state.
The next day, EU leaders will hold an extraordinary summit on migration.
Migrant crisis in Europe: Key dates
13 July: Hungary starts building razor-wire fence on border with Serbia
25 Aug: Germany says all Syrian refugees can apply for asylum there, regardless of which EU country they first entered
2 Sept: Image of body of three-year-old Syrian Alan Kurdi, washed ashore in Turkey, moves public opinion worldwide
12 Sept: Record 4,330 migrants cross into Hungary
13 Sept: In a switch of policy, Germany introduces border controls with Austria — other EU nations later impose their own controls
15 Sept: Hungary enforces tough laws on migrants crossing its border fence, prompting thousands to turn to Croatian route
18 Sept: Croatia transports migrants over its border into Hungary, where Hungary rushes to build new fence