The @nytimesworld team, which covers international events, has about 1.9 million followers and is recognised by the social network as being a "verified account".
But on Saturday it was locked after posting a report about the Canadian prime minister.
The newspaper was told it had violated Twitter's rules about hateful conduct.
The NYT said it had taken Twitter nearly 24 hours to unlock the account and allow it to start posting again.
It normally sends up to 100 tweets a day.