Twitter has started removing verification badges from accounts which already had a blue tick, after announcing they would be part of a paid subscription from 1 April.
The New York Times, along with several other organisations and celebrities, said they would not pay for the tick.
“The real tragedy of @NYTimes is that their propaganda isn’t even interesting”, Mr Musk, who owns Twitter, wrote on the platform.
“Also, their feed is the Twitter equivalent of diarrhea. It’s unreadable,” he added.
The New York Times and Twitter have not yet made any public comments in response to Mr. Musk’s remarks.
According to Twitter’s new policies, accounts that do not pay for it will start to lose the blue ticks that formerly indicated authentic, verified accounts.
Individual accounts must pay $8 (£6.40) per month for a blue verification tick, while organizations seeking verification badges must pay $1,000 (£810) each month to acquire a gold one.
Twitter will make money from the subscription service, but there have been worries raised that it will be impossible to distinguish between real accounts and impersonators without the verification process.
Apart from “few circumstances where this status would be needed for reporting purposes,” a spokesman said, the New York Times stated it would not pay for the authentication of its journalists’ Twitter accounts.
The newspaper, which has over 55 million followers on Twitter, lost its verification symbol after the statement.
Yet, it’s not obvious if all organizations need to subscribe to the program in order to keep their verification.
The New York Times writes, citing an internal Twitter memo, that 10,000 of the most popular Twitter accounts will be excluded from the limits.
Since December, Twitter has added three separate colored verification badges: blue ticks are used for individual accounts, grey ticks are used for multilateral organizations or accounts linked with the government, and gold ticks are used for business organizations.
There are currently several news organizations with gold ticks, such as CNN, the Los Angeles Times, and the Washington Post, all of which have stated they will not pay for Twitter verification.
The gold badge is also present on other New York Times accounts, including New York Times Arts and New York Times Travel.
The blue ticks appear to be being eliminated gradually. The Washington Post, citing former firm employees, speculates that this may be because the procedure is primarily manual.
Celebrities like American basketball legend LeBron James still have a blue tick after declaring he would not pay for Twitter verification. The American rapper Ice-T has voiced similar criticism of the new fee-paying scheme.