Thatcher sent a personal letter, saying that Britain supported India's unity in the face of demands for a separate Sikh homeland.
She also disclosed that police were investigating threats against the safety of Indian diplomats.
According to the Guardian, the letter will cause further debate about Britain's role in the raid among the worldwide Sikh community.
The Indian government had made an apparent request for advice from the SAS in the months leading up to the raid.
The Indian government said about 400 people were killed when Gandhi sent troops into the temple complex in June 1984 in the six-day Operation Blue Star.
Sikh groups, which have called for an inquiry into the British role in the raid, put the death toll in the thousands, including many pilgrims.
The letter, which is in response to two sent by Gandhi on 9 and 14 June, appears to show that she had expressed worries that Sikh 'extremists' could use Britain as a base.
Thatcher also reassured Gandhi that British police were 'devoting considerable resources' to safeguarding Indian government personnel in Britain.
A few months after the letter was sent, Gandhi was gunned down by her own Sikh bodyguards in an act of revenge.
This triggered communal violence, which led to the deaths of thousands of Sikhs across India.