The Lifeline ship carrying 230 migrants says it is still awaiting approval to dock in Malta.
"We ask now, if we are allowed to protect at least from the high waves and the strong wind off the Maltese coast. Many are seasick," the vessel tweeted.
The report came after Italy said it had reached a deal with the archipelago on the ship, which has been stranded for five days after rescuing people off the coast of Libya.
Some other EU countries are expected to help receive migrants.
French President Emmanuel Macron said: "For the last few days we've worked on a European joint solution, and I want to salute here the spirit of responsibility of Maltese PM Joseph Muscat."
"With a few others, France among them, he's forged a solidarity, and I can confirm that France, with some other EU member states, will take up people who are on Lifeline now, when they disembark in a European port, and the French Office for Protection of Refugees is already en route towards Malta to get on with this mission".
Meanwhile, the container ship Alexander Maersk has docked in Sicily.
The Danish-flagged ship rescued 113 migrants off the coast of Libya last Friday and Italy allowed them to disembark at Pozzalo.
Italy's interior minister was asked by journalists why the Maersk container ship was authorised to dock in Sicily.
Interior Minister Matteo Salvini said: "Because we have got good heart, unlike Macron. (But) foreign NGOs with foreign personnel, foreign flagged, with foreign investors will no longer dock in Italian ports".
Italy says other EU countries must help take migrants.
There's still no breakthrough on this issue after 16 EU leaders met in Brussels over the weekend.
A deal may be struck when they meet again at Brussels on Thursday.