Earlier this month, UK forces helped authorities in Gibraltar who believed the tanker was carrying oil to a Syrian refinery in breach of EU sanctions, BBC reports.
The captain said marines made his unarmed crew kneel down on the deck at gunpoint.
Gibraltar police said "minimum force" was used to take control of the vessel.
On 4 July, about 30 marines, from 42 Commando, were flown from the UK to Gibraltar to help detain the tanker and its cargo, at the request of the Gibraltar government.
The vessel's captain, an Indian national who asked not to be named for legal reasons, said he was radioed a police request to board his ship and had lowered his ladder.
But before anyone could board, a military helicopter landed on the ship in "a very dangerous move", he said.
He told the BBC he had identified himself as the captain but the marines ignored him, and instead pointed their guns and shouted "look forward, look forward".
He said: "They didn't care whether I was master… there was no regulations… we had 28 unarmed crew. I was in a state of shock, everybody was in a state of shock.
"How do you come on a ship like this with armed forces and such brute force. For what reason?"
He said the marines could have boarded the ship and simply told him he had been arrested.
The captain agreed to speak to the BBC on condition his name was not used as the crew were advised by Indian High Commission officials to remain anonymous.
Asked whether he felt there was anything illegitimate about his ship or the cargo, he said he had "followed company procedures."
The Gibraltar government said it had evidence which contradicted statements made by the captain, and it would release its own statement soon.
It said it had reason to believe the ship was carrying Iranian crude oil to the Baniyas Refinery in Syria, which the EU says provides financial support to the Syrian government. The refinery has been subject to EU sanctions since 2014.
Iran rejects the allegation, saying the tanker was not headed for Syria and that it couldn't pass through the Suez Canal for its huge size. Tehran accused the UK of piracy, urging the British authorities to release the ship soon.
Carl Bildt, the former Swedish prime minister and co-chair of the European council on foreign relations, pinpointed the ambiguities of the British action in Gibraltar: “The legality of the UK seizure of a tanker heading for Syria with oil from Iran intrigues me. One refers to EU sanctions against Syria, but Iran is not a member of the EU. And the EU as a principle doesn’t impose its sanctions on others. That’s what the US does.”
Iran, as Spain put it as well, sees the move aimed at squeezing Iranian oil exports at the US request. When US National Security Advisor John Bolton heard British Royal Marines had seized an Iranian oil tanker off Gibraltar on America’s Independence Day, his joy was unconfined. “Excellent news: UK has detained the supertanker Grace I laden with Iranian oil bound for Syria in violation of EU sanctions,” he exulted on Twitter.
The seizure of the tanker sparked a diplomatic crisis between the UK and Iran, which has escalated over the past four weeks.
On 19 July, British-flagged oil tanker Stena Impero was seized by the Islamic Revolution Guards Corps (IRGC) in the key shipping route, the Strait of Hormuz, for breaching international maritime rules.
Tehran said the vessel was "violating international maritime rules".
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