Kattner's downfall topples another member of ex-president Sepp Blatter's inner circle at football's world body.
Kattner, a German-Swiss national, had been acting general secretary after previous general secretary Jerome Valcke was also dismissed for irregularities.
"Kattner has been dismissed from his position effective immediately," the world body said in a statement.
"FIFA's internal investigation uncovered breaches of his fiduciary responsibilities in connection with his employment contract," it added.
"There was enough to determine there was a breach of his responsabilities and to take action against Mr Kattner," a source close to an internal FIFA investigation said.
The source said the money came from bonuses under a contract whose terms were kept secret from FIFA audit committees.
The world body indicated that Kattner is the subject of an outside inquiry.
"FIFA will not comment further on any of the details, but will continue its cooperation with the relevant authorities," said the statement.
Swiss prosecutors are already investigating Blatter, who is serving a six year ban imposed by FIFA, and Valcke.
Blatter is under investigation for making a "disloyal" payment of USD 2 million to ex-UEFA leader Michel Platini, who has also been banned from football activities.
The action is a new blow to FIFA's reputation as it seeks to redeem its scandal-tainted name under new president Gianni Infantino who was elected in February.
Infantino only this month named Fatma Samoura as its new general secretary. Samoura is the body's first woman secretary general and FIFA also wanted her United Nations background to give a sign of football's new direction.
Infantino has repeatedly said he wants to bring a new era of "transparency", "honesty" and "professionalism." But Kattner's dismissal is a new sign that FIFA's past misdeeds have still not all been brought out into the open.