Panama's maritime authority has started withdrawing the registration of an oil tanker MT Riah that was towed to Iran after it disappeared from ship tracking maps in the Strait of Hormuz on July 14.
Panama began the process on Friday after an investigation determined the tanker had "deliberately violated international regulations" by not reporting any unusual situation, the authority said.
"We roundly condemn the use of Panamanian flagged ships for illicit activities," the maritime body said.
Panama, which has the largest shipping fleet in the world, has recently withdrawn flags from dozens of vessels, some of which were operated by Iran.
It is not clear which country or company owns and operates the Riah.
The latest development follows the British seize of the Iranian oil tanker Grace 1 on accusations of violating European sanctions on Syria.
Panama said the ship had been removed from its registry on May 29.
Iran's Supreme Leader Ayatollah Khamenei branded the British action "piracy", and the country threatened to retaliate.
Iran recently said it towed a vessel into its waters from the strait after the ship issued a distress call. Although Tehran did not name the vessel, the Riah is the only ship whose recorded movements appear likely to match that description.
US officials have said they are unsure whether the tanker was seized by Iran or rescued after facing mechanical faults as Tehran asserts, creating a mystery at sea at a time of high tension in the Arabian Gulf.
Earlier this month, Panama's maritime authority said it would withdraw its flag from more vessels that violate sanctions and international legislation, following the removal of about 60 ships linked to Iran and Syria from the Panamanian registry in recent months.
Washington has called for greater security for ships in the Gulf.