Mr Musharraf was the then country's President and Mr Sharif had just returned from exile.
The Dawn on Wednesday quoted Mr Sharif as saying that he didn't believe in making clandestine deals with people who had ruined people's aspirations. He said his family did not want to leave Pakistan after the Musharraf-led military coup but was forced to go into exile by the military dictator.
"We left the country in a miserable condition and were not allowed to return for a long time," he said.
The Prime Minister noted that Mr Musharraf, a former Pakistan Army chief, was now facing a similar fate and had left the country in disgrace.
Mr Sharif was toppled by Musharraf in a 1999 coup, after which Sharif and his family went to live in Saudi Arabia.
However, Mr Sharif's assertions were disputed by former Musharraf aide and All Pakistan Muslim League member Ahmed Raza Kasuri, the Dawn reported.
"I have been working with General Musharraf for a long time and I have never heard any such thing," he said.