In a statement on Friday, the Frankfurt prosecutor's office said it had also filed a request to involve the DFB in the criminal proceedings which could lead to fines.
The office did not name the four officials but said they were aged between 67 and 76 years.
The three senior DFB officials are accused of arranging for incorrect tax returns to be submitted for 2006 to enable the association to avoid paying around 13.7 million euros (12 million pounds) in tax, the office said.
The tax return included a 6.7 million euro payment from the DFB to FIFA for a World Cup event, although the funds were in fact used for another purpose and should not have been offset against tax, it said.
FIFA said in an emailed statement it was "publicly known" that the Frankfurt prosecutor's office had been conducting the investigation.
"FIFA takes note that the Public Prosecution Office of Frankfurt am Main has brought charges in this context against several former DFB officials and a former FIFA official," it said.
"FIFA supports the investigation and co-operates with the relevant authorities to help clarify the relevant facts."
The DFB could not immediately be reached for comment.
The payment in question has triggered several investigations in the past two years over allegations it had been used as a slush fund to buy votes in favour of Germany's bid to host the 2006 tournament.
A DFB-commissioned investigation in 2016 said the sum was the return of a loan via FIFA from former Adidas chief Robert Louis-Dreyfus.
Last October, the tax office ordered the DFB to pay 19.2 million euros in back taxes related to the payment for the 2006 World Cup.
(Reporting by Caroline Copley; Additional reporting by Brian Homewood; Editing by Toby Chopra and David Holmes)
