The 45-year-old German took over as acting general secretary after Jerome Valcke was sacked for irregularities.
The dismissal is not connected to the payment made to Michel Platini by former president Sepp Blatter in 2011.
Former Fifa vice president Platini and Blatter were last year found guilty of ethics breaches over the 2m Swiss Franc (£1.3m) "disloyal payment".
Uefa president Platini, 60, resigned from European football's governing body after failing to have a six-year ban from football overturned.
Blatter, 80, is still waiting to hear the outcome of his appeal to the Court of Arbitration for Sport.
Valcke, 55, was given a 12-year ban from football in February for his alleged involvement in a scheme to profit from the sale of World Cup tickets.
Kattner joined Fifa in 2003 as director of finance, becoming deputy secretary general in 2007.
His salary and bonuses were part of a contract that was unseen by relevant Fifa committees.
No other current Fifa directors are believed to be involved.
United Nations official Fatma Samoura has already been named as Fifa's new permanent secretary general.
The 54-year-old Senegalese woman is set to start her role next month.
In Sierra Leone, the Anti Corruption Commission has started investigating the Sierra Leone Football Association (SLFA) for corruption.