Morsi, the country's first freely elected president, was ousted on July 3, 2013 by then army chief and now President Abdel Fattah al-Sisi after mass street protests against the Islamist's one-year rule.
Several pro-Morsi satellite channels aired on Friday audio recordings of a man identified as General Mamdouh Shahin, legal adviser to then army chief Sisi, warning other senior officials in Sisi's office that the case against Morsi would collapse if certain documents were not "forged".
In one of the recordings leaked to the media, Shahin is heard telling the officials, including interior minister Mohamed Ibrahim, how the authorities did not detain Morsi in interior ministry-run prisons, and instead held him in a building belonging to the army immediately after his ouster.
In another tape, Shahin allegedly tells the other officials that documents had been "forged" so that the case against the Islamist would not be jeopardised.
The authenticity of the recordings could not be independently verified.
The authorities have repeatedly said Morsi's ouster was not a "coup" as claimed by his Muslim Brotherhood, but a decision taken after mass street protests that rocked Cairo and other cities on June 30, 2013.
For weeks after his ouster Morsi's whereabouts were unknown, with his supporters repeatedly asking where he was being held.
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"The military has not confirmed where they (Morsi and aides) are currently held," Human Rights Watch said on July 8, 2013, five days after his ouster.
The taped conversations went viral on the Internet and social networks like Twitter and YouTube on Friday.
The prosecutor general accused the Muslim Brotherhood of "fabricating" the recordings and launched an investigation into it.
The Brotherhood movement "uses the media supported by foreign entities ... and uses advanced technology to fabricate phone calls and attribute them to public figures and leaders ... to sow chaos and disrupt security," it said in a statement.
This was an attempt to "influence the judges who are reviewing important criminal cases against the terrorist elements of the Muslim Brotherhood."
Vowing to fight such "crimes", it ordered an "extensive investigation to find those responsible for fabricating these recordings".
The authorities have been waging a brutal crackdown against Morsi supporters since his ouster.
At least 1,400 have died in clashes with police and more than 15,000 jailed in the crackdown, while top Brotherhood leaders including Morsi are facing trials punishable by death.