Sea Watch, which runs the Moonbird aircraft, condemned the move, accusing authorities of grounding the plane during the “deadliest days” in the Mediterranean since records began.
The German NGO said the plane had been involved in the rescue of some 20,000 people since it began operating.
A Maltese government spokesman confirmed the aircraft had been grounded and said a full statement was expected later in the day.
“About 1,000 would have drowned for sure if our Moonbird would not have found their sinking boats at the last second,” Sea Watch wrote on Twitter. “Now this life saving asset is blocked as well by EU authorities, even if we face the deadliest days since records started.
“Witnesses are obviously not welcome.”
The ban appeared to be part of efforts by both Malta and neighbouring Italy to make it near impossible for NGOs to use the countries as bases to help rescue migrants adrift off the nearby Libyan coast.
It comes just days after the European Union announced a significant hardening of its stance on migrant rescues in the Mediterranean.
After a summit in Brussels, EU leaders backed the approach of Italy’s new populist government, suggesting boats should stay away and could be breaking the law by picking up those in distress.
A communiqué issued by the European Council warned the vessels’ operators they should defer to the Libyan coastguard, which NGOs say amounts to “deliberately condemning vulnerable people to be trapped in Libya, or die at sea”.
On Wednesday, a rescue ship carrying 60 migrants arrived in a Spanish port after being refused entry by Italy and Malta, the second time in a month that a humanitarian group has been forced to travel for days to unload people rescued in the central Mediterranean.
The Open Arms ship docked in the northeastern port of Barcelona, where the group – including five women, a nine-year-old and four teenagers – will be going through health checks and identification procedures.
The Spanish aid group Proactiva Open Arms said the migrants had come from 14 countries and were in good health.
More than 500 people died in the Mediterranean after the Aquarius, another rescue ship, was blocked from ports in Italy and Malta in June, according to Doctors Without Borders.
Last week Malta said it had closed its harbours to all NGO ships after allowing a vessel operated by the German charity Mission Lifeline to dock and disembark 133 migrants.
Italy and Malta had criticised the ship for defying Italian coastguard orders and picking up the migrants rather than leaving the task to the Libyan Coastguard.
Another NGO rescue ship, the Sea Watch III, was blocked from leaving Valletta Harbour on Sunday, for undisclosed reasons.
Malta, like Italy, has insisted that NGO ships must not obstruct national coastguards from rescuing migrants.
Additional reporting by agencies
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