Pakistan has often been described as a dangerous country for journalists and the security of media personnel was also raised by Committee to Protect Journalists, a media advocacy group, during a meeting with Premier Nawaz Sharif this week.
The Prime Minister pledged to continue to expand Pakistan's media freedoms and address the insecurity plaguing the country's journalists.
He also promised to ease visa and travel restrictions on foreign journalists working in the county, a statement by the group had said. But the media is working with caution.
The nearly 5,000-word article, an excerpt from a forthcoming book by NYT reporter Carlotta Gall, appeared in the daily's magazine in the US but was missing from the paper's edition in Pakistan yesterday.
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In its place was a large blank box on the front page and a full-page ad by its Pakistani partner the Express Tribune on the second page.
This led to a huge outcry on social media with many alleging that the country's spy agencies were behind it.
However, a senior editor of the paper pointed out that in most likelihood it was self-censorship.
She added, "While we understand that our publishing partners are sometimes faced with local pressures we regret any censorship of our journalism".
The daily has been under pressure after three of its employees were shot down by the Pakistani Taliban in January.
The paper, which was known for hard hitting opeds, has now a rule under which articles on certain subjects including the Taliban and a leading politician, who is not from the ruling PML-N, have to be cleared by the editor.