"What I want is to intervene for humanitarian reasons, not to interfere in a court ruling,"Mr Morsi told members of the Egyptian community in New York, where he was attending meetings of the UN General Assembly.
Abdul Rahman was convicted in 1995 for his role in the attack, plotting to bomb other New York targets including the United Nations and a plan to assassinate former Egyptian president Hosni Mubarak.
He was sentenced to life in prison.
"We want his family to be allowed to visit him and to serve his sentence in Egypt as part of a prisoner swap between Egypt and the United States," Mr Morsi said in statements carried by the official MENA news agency.
The Egyptian President, who emerged from the powerful Muslim Brotherhood, said that "recent incidents around the US embassy in Cairo have delayed efforts in this regard," MENA reported.
Mr Morsi was referring to angry protests on September 11 over a film produced in the United States mocking Islam and portraying the Muslim Prophet Mohammed as violent and immoral.
Protesters managed to scale the wall of the embassy, tear down the US flag and replace it with a black Islamic flag.
On June 29, on the eve of his inauguration, Mr Morsi told a rally in Cairo that he would work to free Abdul Rahman, commonly refered to as "the blind sheikh".
"I will do everything in my power to secure freedom for detainees, including Sheikh Omar Abdul Rahman," Mr Morsi said.