The Chinese vessel Xiang Yang Hong 03, which is en route to the Maldives, will only make a port call "for rotation of personnel and replenishment" while in its waters, the ministry said in a statement.
Such vessels are not officially military ships but India and other countries worry about the military use of their oceanographic research.
Its presence is likely to raise concern in New Delhi, which has previously viewed such vessels close to its shores as problematic.
"The Maldives has always been a welcoming destination for vessels of friendly countries, and continues to host both civilian and military vessels making port calls for peaceful purposes," the foreign ministry said.
Permission to allow the ship to dock could further vex the ties between traditional friends New Delhi and Male, which have soured since President Mohamed Muizzu took office in November promoting an 'India Out' campaign.
Both New Delhi and Beijing vie for influence on the tiny Indian Ocean nation but the new government in Male is pivoting towards China and has asked India to withdraw its nearly 80 troops stationed there.
New Delhi has in the past flagged similar visits by other Chinese research vessels with its neighbour Sri Lanka, which has denied permission for such vessels to dock at its ports since 2022.
Chinese state media has said research by such vessels should not be called threatening.
(Reporting by Uditha Jayasinghe; Editing by Angus MacSwan)
