Pakistan says it has completely dismantled the underground network of disgraced nuclear scientist, Abdul Qadeer Khan.
Japan is concerned about nuclear proliferation
The foreign minister, Khursheed Kasuri, said reports of AQ Khan's network still being active were baseless.
His statement came at a joint news conference with his visiting Japanese counterpart, Taro Aso.
His statement came as China reiterated that its nuclear co-operation with Pakistan was for peaceful purposes.
Recently, Britain's Financial Times newspaper had reported that Pakistan was in talks to buy between six and eight nuclear reactors from China in a deal worth up to $10bn (£5.8bn).
Pakistan has denied this report.
The BBC's Zaffar Abbas says that Pakistan is conscious of Japan's specific concerns about proliferation and the government has said it is really sorry about the past.
In 2004 AQ Khan admitted to passing nuclear secrets
"Pakistan is very sorry and is very upset and has taken all appropriate action in dismantling the underground network," Mr Kasuri said.
Earlier in the week Britain's Guardian newspaper quoted a European Union intelligence report saying that Pakistan's underground network was still very active.
AQ Khan is regarded by most people as the father of Pakistan's nuclear bomb, but he fell from grace after he admitted in 2004 passing nuclear secrets to countries like Iran, Libya and North Korea.
Mr Aso also praised Pakistan for providing the necessary information on the secret nuclear proliferation network and Dr Khan to Japan.
Both the countries have also signed an agreement on an emergency earthquake loan of $100m and an additional grant of $55m for the earthquake-hit areas.