An official in eastern Kasur district made the decision after objections were filed, including charges of violating the constitution and his oath as army chief.
Gen Musharraf has the right to appeal and has also filed nomination papers in three other constituencies.
But this may affect those decisions.
Six objections were brought against Gen Musharraf by a local lawyer in Kasur. Election tribunals will begin to hear appeals next week.
In a parallel development, the PML-N party of former Prime Minister Nawaz  Sharif - ousted by Gen Musharraf when he took power in a coup in 1999 -  has challenged Mr Musharraf's eligibility to contest elections.
The former military ruler faces a string of charges dating from his final months in office - but he has been granted protective bail in these cases, which means he cannot be immediately arrested.
He is accused of failing to provide adequate security for former PM Benazir Bhutto ahead of her assassination in 2007.
He is also wanted in connection with the murder of a Baloch tribal leader, Nawab Akbar Bugti, and for sacking the entire higher judiciary in November 2007.
The former president has described the cases against him as "baseless" and politically motivated.
His supporters were defeated in parliamentary elections in February 2008, and Gen Musharraf resigned in August that year under threat of impeachment, living in  London and Dubai until his return last month.
In a separate development, a court in Pakistan  sentenced a former provincial minister to two years in prison for falsely declaring that he was a graduate.
Mir Ali Jattak, a former minister of Balochistan province, is the seventh politician to be jailed in recent days for fraudulently claiming to hold a degree.
These lawmakers  are believed to have submitted "fake" degrees because of  a 2002 law that required members of parliament to be college graduates - the law has since been abolished.
Officials have rejected nomination papers for Pakistan's ex-military ruler Pervez Musharraf to stand as a candidate in forthcoming polls.