The authorities said a court was expected to decide on the issue soon.
A defiant Mr Aboutrika said he would stay in Egypt to work for prosperity.
Mr Aboutrika publicly endorsed the successful 2012 presidential bid by Mohamed Morsi, a Brotherhood member. Mr Morsi was ousted by the army in 2013.
An ensuing crackdown on Mr Morsi, Egypt's first freely-elected leader, and Brotherhood members has left hundreds of people dead and thousands in jail.
The Egyptian authorities said they had seized Mr Aboutrika's assets - including his shares - in a number of companies.
In response, the 36-year-old former midfielder tweeted: "Confiscate the money or confiscate the money's owner, I will not leave the country, and I will continue to work for its prosperity."
If an investigation proves that he has been funding the Muslim Brotherhood the whole case will go to court, the BBC's Inas Mazhar reports.
Our correspondent says Mr Aboutrika may even be detained temporarily while the investigation continues.
She adds that Egyptians are split on the issue, with the footballer's numerous fans supporting him and others siding with the authorities.
Mr Aboutrika - a star of Cairo's al-Ahly club and the national team - retired in 2013.
During his career he was four times named as Africa's best player of the year.
The Egyptian authorities have seized assets of former national football star Mohamed Aboutrika, amid allegations that he helped fund banned Islamist movement the Muslim Brotherhood.