An NGO operating a migrant rescue vessel ship said on Tuesday it had been denied entry into Malta for re-supply and a change of crew.
In a tweet, the Medecins Sans Frontieres said its vessel Aquarius had been barred from entering the island and no explanation was provided.
The government or the port authorities have not yet reacted to the tweet.
In another tweet later, MSF said the Aquarius was now heading towards Marseille.
"This back and forth is far from ideal and keeps us away from the search and rescue zone for an extended period, for a simple port call."
Only last Saturday, the government denied claims made by the Aquarius, the ship at the centre of a recent migrant dispute with Italy, that the Maltese authorities have refused to allow it permission to dock at any of its ports in the future.
The BBC, which had a reporter on board the rescue ship, had reported that a decision to bar the vessel from entering applies "whether or not" it has migrants onboard.
The development came minutes after Malta appeared to have budged to accept a group of 239 migrants stranded at sea for four days on condition that the asylum seekers are distributed among "willing" EU states.
The Aquarius was at the centre of a standoff between Italy and Malta earlier this month when it was denied entryby both Italy and Malta to disembark migrants. It later disembarked the migrants in Spain.
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