ISLAMABAD, Pakistan—Pakistan lifted a travel ban on a prominent journalist on Friday, days after barring him from leaving the country over his newspaper article alleging rifts between the government and the military.

The Interior Ministry banned Cyril Almeida from leaving Pakistan on Monday after he published an article about a meeting between the country’s top civilian and military leaders in which he wrote that government officials blamed the military for inaction against extremists, and the resulting diplomatic pressure on Pakistan.

The government and military said the article was fabricated. Interior Minister Chaudhry Nisar Ali Khan said Thursday that the article, while false, reinforced the narrative of Pakistan’s enemies that the country doesn’t do enough to combat some terrorist groups. The military said in a statement Friday that the story was “a breach of national security.”

Mr. Almeida is an assistant editor and columnist at Dawn newspaper, which stood by the article.

Pakistan’s military has for decades faced accusations of supporting militant groups as proxies in Afghanistan and against India, a charge it denies.