The Seabed Constructor, hired in January for a fresh search for the missing plane, turned off its location transponder for three days without explanation early this month, sparking a slew of speculation, including that it had gone on a treasure hunt.
"There is nothing to be worried about. We urge family members not to listen to rumours or fake news," Transport Minister Liow Tiong Lai told AFP.
He said the Seabed Constructor "is doing fine" and that "the search will continue as planned".
MH370 disappeared in March 2014 with 239 people -- mostly from China -- on board while en route from Kuala Lumpur to Beijing.
An earlier Australia-led search -- the largest-ever in aviation history -- scoured 120,000 square kilometres (46,000 square miles) of a remote region of the Indian Ocean for 28 months but found no trace of the aircraft, and the hunt was suspended last January.
Last month the Malaysian government hired Ocean Infinity, a private firm, to head a fresh hunt for the missing plane.
Search ship Seabed Constructor has deployed high-tech underwater drones to cover a new area of about 25,000 square kilometres in the Indian Ocean.
But 10 days into into its mission, it switched off its Automatic Identification System without any explanation.
Liow, however, clarified that the vessel had returned to the Australian port of Fremantle for a scheduled refuelling.
Some relatives of the missing passengers and crew of MH370 said they had been left in the dark over why the ship disappeared from monitors.
"Yes. We want to know what is the reason for this. In MH370 the transponder was switched off. Why? We are curious to know why and what happened? So far we have not got any explanation," Jacquita Gonzales, the wife of MH370 cabin crew supervisor Patrick Gomes, told AFP
She added "if they can explain more, then we will be at ease".
KS Narendran, who had a relative on MH370, called for more information and greater transparency.
"Silence, delays in communication, deflection, obfuscation and other devices to manage or massage the messaging will do little to build trust and credibility," he said in an email to AFP.
"I therefore believe it is best to be transparent, timely in communicating, and not measly with detail. Affected families are not fragile. They have waited long and have known disappointment and heartbreak."
V.P.R. Nathan, whose wife Anne Daisy was on the plane, saw nothing sinister going on.
"The ship is not obliged to tell anyone of its location. There are a lot conspiracy theories out there. Please ignore them," he told AFP.
Liow said family members were being kept updated on a weekly basis by officials from the Department of Civil Aviation.
"I am happy with the progress of the search. It is moving very fast. We really hope we can find the wreckage," he said.
Only three confirmed fragments of MH370 have been found, all of them on western Indian Ocean shores, including a two-metre wing part known as a flaperon.
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