Advocate Javed Kasuri had raised objections over Musharraf's candidacy, citing Articles 62 and 63 of the Constitution that lay down rules for qualification and disqualification for contestants for the Majlis-e-Shoora (parliament), a report said.
Accepting the objections, the returning officer rejected the nomination papers.
Musharraf filed papers to contest elections from four parliamentary seats - Karachi, Islamabad, Chitral and Kasur.
Located adjacent to the India-Pakistan border, the city of Kasur is 55 km from Lahore and is one of the oldest cities of the country.
Meanwhile, the Pakistan Muslim League-Nawaz (PML-N) has also sought Musharraf's disqualification by the Election Commission, citing his ineligibility due to alleged involvement in four cases.