The petition, submitted to the House by a member, Lovette Idisi, said she has been “incessantly harassed” by the anti-graft agency.
Dame Jonathan also alleged that operatives of the Department of State Services (DSS), National Drug Law Enforcement Agency (NDLEA) are threatening her life.
She added that operatives of the agencies “broke” into her Abuja home twice in her absence.
The former First Lady also stated that EFCC froze her children’s and relatives’ accounts, credited to media reports negatively affected her husband’s reputation.
Reading the petition before the House, Idisi slammed the EFCC.
He said the EFCC’s actions towards the former First Lady were contrary to Section 36 of the 1999 Constitution, which presumed that individuals are presumed innocent until proven guilty.
He said: “This petition is in line with Section 36 of the 1999 Constitution which dictates that every citizen is presumed innocent until proven guilty.
“The constant harassment of the former First Lady is contained in a petition which emanated from her, that was sent to my office.
“With the leave of the House I seek your permission to lay the petition before the House.”
Speaker Yakubu Dogara, who presided over plenary, referred the petition to the Committee on Public Petitions.