The attorney general said Matthew Rosenberg's article about the country's election stalemate was "contrary to the national interests, security and stability of Afghanistan" and ordered him to leave the country within 24 hours.
The order was the first expulsion of a journalist from Afghanistan since the Taliban regime was ousted in 2001, highlighting fears for press freedom after 13 years of international aid funding and development.
Rosenberg tweeted an image of the attorney general's statement that said: "This is not the first time that this reporter has published propaganda, and it appears that he has links with intelligence and spy agencies."
The New York Times article on Tuesday said that senior Afghan officials were discussing forming a committee-run "interim government" to end a stand-off over the disputed result of the presidential election.
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Any such move that would end international hopes that democracy would be a flagship legacy of the costly US-led military and civilian intervention in Afghanistan.
The impasse -- centred on fraud allegations -- has threatened to revive the divisions of the 1990s civil war, when ethnic conflict ravaged Afghanistan and allowed the Taliban to seize power.
"This... Is a regrettable step backward for the freedom of the press in this country," US ambassador James Cunningham said in a statement.
"There is no mistaking the signal this sends to all journalists."
Cunningham added he had expressed the US position directly to Karzai, who has had a series of bitter arguments with Washington in recent years.