Malaysia had previously expressed concern about the conflict in Ukraine but stopped short of condemning Russia. It has not commented on the international sanctions imposed on Russia over the invasion.
The ministry's statement, which attributed the decision to block the ship to port authorities rather than the government, suggested "an attempt to split the difference" in placating both Russia and the United States, said Euan Graham, senior fellow at the International Institute for Strategic Studies.
"It's a pragmatic move to try and maneuver between two large countries … as I suspect the US is applying significant pressure behind the scenes on Malaysia to observe sanctions," he told Reuters.
According to the United States, Linda is owned by PSB Leasing, a unit of Russian lender Promsvyazbank, which has also been hit by international sanctions. Provsyazbank, however, has denied that its subsidiary owned the vessel.
A US advocacy group has said Linda was also suspected to be transporting Iranian oil, a target of other US sanctions.