Malta's PM said the Lifeline would arrive on Wednesday, after his country and seven other EU states agreed to take a share of those on board.
Joseph Muscat added that genuine asylum seekers would be allowed to stay.
Italy's new government has closed its ports to rescue ships operated by charities in the Mediterranean.
The dispute over the Lifeline echoes that which surrounded the Aquarius, whose 630 migrants were finally taken to the Spanish port of Valencia last week, after being blocked by Italy and Malta.
Mr Muscat said on Wednesday: "I believe the vessel will reach our shores this evening."
Italy, Luxembourg, the Netherlands, Portugal and Ireland, Belgium and France had also agreed to receive some of the migrants, he added.
Mr Muscat also said the vessel would be impounded pending an investigation. The Maltese authorities suspect the captain defied an Italian order to let the Libyan coastguard pick up the migrants.
Earlier, French President Emmanuel Macron said France would take in "a few dozen individuals", but also said the Lifeline had "acted against all rules".
Italian Interior Minister Matteo Salvini told the BBC that illegal migrants were risking their lives by making the journey.
A sick passenger was evacuated to Malta from the Lifeline on Monday night.
The German charity Mission Lifeline tweeted that conditions were worsening for the migrants on board.
Meanwhile, 108 migrants have been taken ashore in Italy from a Danish container ship. The Alexander Maersk was allowed to dock in the Sicilian port of Pozzallo.
EU leaders face tough negotiations on the migrant crisis at a Brussels summit on Thursday.
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