Twitter said it has secured the compromised account known as @narendramodi_in.
The affected account is linked to PM Modi's personal website and has more than 2.5 million followers.
"We are actively investigating the situation. At this time, we are not aware of additional accounts being impacted," a Twitter spokesperson said in a statement.
According to Twitter, this breach was not due to a compromise of its systems or service.
"There is no indication or evidence of any correlation between this account compromise and the incident that took place in July," the company said in a statement shared with IANS.
Twitter faced a mega crypto hack in July that spread a Bitcoin scam by hijacking accounts of high-profile celebrities, politicians and businesses as a result of a phone spear phishing attack.
"I appeal to you all to donate generously to PM National Relief Fund for Covid-19, Now India begin with crypto currency, Kindly Donate eth (Ethereum) 0xae073DB1e5752faFF169B1ede7E8E94bF7f80Be6 (sic)," read one tweet from the hackers.
Ethereum is the second-largest cryptocurrency platform by market capitalisation, behind Bitcoin.
Another tweet read: "I appeal to you all to donate generously to PM National Relief Fund for Covid-19, Now India begin with crypto currency, Kindly Donate Bitcoin to 0xae073DB1e5752faFF169B1ede7E8E94bF7f80Be6 (sic) #eth #crypto".
The tweets were later taken down by Twitter.
In July, the attackers targeted 130 Twitter accounts, ultimately tweeting from 45, accessing the DM (Direct Messages) inbox of 36, and downloading the Twitter data of seven accounts.
The incident raised concerns around Twitter tools and levels of employee access.
The accounts of major public figures including US Democratic presidential candidate Joe Biden, Barack Obama, Elon Musk, Bill Gates, Jeff Bezos, Apple and Uber were simultaneously hacked by attackers to spread a cryptocurrency scam.