The decision has been taken by the Union Cabinet at a meeting presided over by Prime Minister Narendra Modi.
The compensation to the families of the riot victims will be given in addition to what they have so far received from the government and other agencies, official sources said.
Of the 3,325 victims, 2,733 were killed in Delhi alone while rest of the victims were from Uttar Pradesh, Haryana, Madhya Pradesh, Maharashtra and other states.
The fresh compensation, which will cost the exchequer Rs 166 crore, sources said.
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The anti-Sikhs riots were triggered following the assassination of the then Prime Minister Indira Gandhi by her Sikh bodyguards on October 31, 1984.
In 2006, the UPA government led by Prime Minister Manmohan Singh had announced a package of Rs 717 crore which included monetary compensation of Rs 3.5 lakh to the kin of each killed in the riots besides financial assistance to the injured and those who had lost their property.
The most affected regions were the Sikh neighbourhoods in Delhi.
Some of the anti-Sikh riot cases are still continuing in courts and many Sikh organisations have alleged that the key conspirators of the violence were at large and victims have not yet got justice.
In 2005, then Prime Minister Manmohan Singh had apologised for the 1984 anti-Sikh violence saying Gandhi's assassination was a "great national tragedy" and what happened subsequently was "equally shameful".
"I have no hesitation in apologising to the Sikh community. I apologise not only to the Sikh community, but to the whole Indian nation because what took place in 1984 is the negation of the concept of nationhood enshrined in our Constitution," he had said.