But Amaechi, who is a former governor of Rivers State, said Jonathan is not being honest, adding that he fell out with the ex-president too.
Jonathan, however, acknowledged that there was a conflict between his wife, Patience, and Amaechi.
He said he tried to settle the feud but the two would not give room for a truce.
The ex-president revealed this in a book titled, 'Against the Run of Play,' written by the Chairman, Editorial Board of ThisDay, Olusegun Adeniyi.
"Jonathan told me that Amaechi's problem was not with him but rather with his wife and that, at a point, he tried to reconcile them," the book stated.
Reacting to Jonathan's statement, Amaechi, who is a former governor of Rivers State, said the ex-president is not being honest.
While he admitted that he locked horns with Patience, the ex-governor said he had a disagreement with Jonathan too.
Amaechi said the cause of his grudge with Jonathan was his (GEJ) repeated illegal and excess deduction from the federation account.
He said, "I could not surrender my mandate to a woman (Patience) in Abuja, even if such a person was the wife of the President…that basically was my sin with Dame Patience Jonathan.
"If in one year, you took about N300bn from the federation account to pay for subsidy and the next year, you are taking almost N2tn for the same thing when fundamentals had not changed, then serious questions should be asked.
"And as NGF (Nigerian Governors Forum) chairman, it was my responsibility to ask those questions and Jonathan took them personal."
The book will be launched today, Friday, April 28.