"The focus of our concern is that this is a potential unauthorised modification of a maritime anti-ship defensive capability to an offensive land-attack missile," a senior administration official told the paper.
"When we have concerns, we act aggressively."
A senior Pakistani official called the accusation "incorrect", saying that the missile tested was developed by Pakistan, just as it had modified North Korean designs to build a range of land-based missiles that could strike India, according to the newspaper.
Suspicious missile test
US intelligence agencies allegedly detected of a suspicious missile test on April 23, which was never announced by the Pakistanis and which appeared to give it a new offensive weapon.
US military and intelligence officials suspect Pakistan of modifying the Harpoon sold to them in the 1980s during the Reagan administration as a defensive weapon, which would violate the Arms Control Export Act.
Pakistan denied the charge and said it had developed the missile, the New York Times said.
The missiles would bolster Pakistan's ability to threaten India, stoking fears of heating up the two nations' arms race.
The charges come as the administration of Barack Obama, the US president, is seeking congressional approval for $7.5bn in aid for Pakistan over the next five years.