Mursi was speaking after replacing powerful head of the armed forces Field Marshal Mohammed Hussein Tantawi and chief-of-staff Gen Sami Anan.
Egyptian media today hailed 60-year-old Mursi's move as "revolutionary" and aimed at curbing the power of the Supreme Council of the Armed Forces (SCAF).
76-year-old Tantawi was the head of SCAF, which ruled the country following ouster of longtime ruler Hosni Mubarak in February 2011. Tantawi was defence minister for nearly two decades under Mubarak.
"The decisions I took today were not meant ever to target certain persons, nor did I intend to embarrass institutions, nor was my aim to narrow freedoms," Mursi said hours after presidential spokesperson Yasser Ali announced the move in a televised statement.
"I did not mean to send a negative message about anyone, but my aim was the benefit of this nation and its people," Al Jazeera quoted Mursi as saying.
Mursi praised the work of the armed forces, saying his decision would free them to focus on their professional tasks.
Mursi also annulled a constitutional addendum that was issued by the SCAF on June 17 under which the Army took control of legislative powers and limited the president's powers, after a Supreme Court verdict dismissed the elected parliament. He also amended the SCAF-issued March 30, 2011, Constitutional Declaration. (More)