"I am forced to leave for reasons that have nothing to do with the club," Puche was quoted as saying in the Spanish media on Tuesday.
The legal investigation, which centres on the alleged smuggling of contraband tobacco, hit the headlines when Puche was detained briefly by Spanish authorities at the end of 1999.
"I leave happy with all that has been achieved over the past few years. But I have to go because of this investigation and I do not want the club to get mixed up in the affair.”
"Now I need to concentrate on defending my business," he added.
Puche took over as Malaga president in September 1997 when the Andalucian club was in the third division.
In successive seasons Malaga won the third and second division titles and then finished 12th in its first season in the top flight for 10 years.
Malaga are currently seventh in the first division, two points behind Celta Vigo, and still have an outside chance of securing a slot in next year's UEFA Cup.
Fernando Puche has quit as president of Spanish first division club Malaga because of a legal investigation into his business interests.
