The National Assembly is due to hold its inaugural session on Saturday.
According to the Supreme Court his papers were rejected because his degree was fake.
Although he filed a petition but he cannot be sworn in until the court announces a verdict on the case, the chief justice said.
The Supreme Court had allowed Agha to contest elections on temporary basis, however he has been barred from swearing in as a member of the assembly.
The swearing in ceremony of National assembly will be held on Saturday.
Correction: An earlier version of the story incorrectly mentioned that the Maulvi Muhammad Agha was an MPA.
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