"No modification has been made to the missiles under reference," Foreign Office spokesman Abdul Basit said.
Basit said the accusations being made were a part of conspiracy to malign the image of Pakistan and its armed forces internationally.
According to The New York Times, top US administration and Congressional officials believe that Islamabad has illegally modified American-made missiles to expand its capability to strike land targets, a potential threat to India.
Officials alleged that Pakistan has customized conventional Harpoon antiship missiles, which were provided to it by the Reagan administration as a defensive weapon in the cold war era.
"There's a concerted effort to get these guys to slow down. Their energies are misdirected," said one senior administration official.
Meanwhile, Pakistan's Envoy to the US, Hussain Haqqani, has also denied the allegations. "The accusations are incorrect and based on wrong intelligence," The Daily Times quoted Haqqani, as saying.