The Berlin-born midfielder, who has dual German and Tunisian citizenship and has played for the Tunisia national team and German national youth teams, joined Darmstadt this season. He previously played for Hamburg SV and Hertha Berlin.
Ben-Hatira, 28, has made public statements of support for Ansaar International, which describes itself as an aid organisation supporting Muslims in Germany and abroad.
But German authorities accuse the group of supporting a Salafist network in Germany, and its domestic intelligence service has said it is monitoring the group, according to media reports.
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In recent months, Darmstadt fans have taken issue with Ben-Hatira over this matter, distributing leaflets in the stadium last week urging the player to distance himself from Ansaar International.
"After analysing the overall situation there is no sense to continue the collaboration between the two sides," said Darmstadt President Ruediger Fritsch in a statement late on Wednesday.
"Darmstadt 98 considers Ben-Hatira's personal humanitarian involvement for this organisation as wrong. Darmstadt 98 wishes Aenis Ben-Hatira, who has always behaved outstandingly and acted as a role model at our club, all the best for his sporting future."
Ben-Hatira, who has also played for German national youth teams, said he was proud of his work.
"There are few people who carry a heavy responsibility but can still look themselves in the mirror and be proud," he said on his Facebook page, adding he would comment further in the coming days.
German officials say there are around 9,000 suspected hardline Islamist sympathisers in Germany, compared with 7,000 at the end of 2014. Vice Chancellor Sigmar Gabriel has said he wants mosques run by Salafists to be banned and their networks broken up.
A Tunisian who killed 12 people in a Christmas market attack in Berlin last year had reportedly been in touch with Salafist preachers.
(Reporting by Karolos Grohmann; Editing by Raissa Kasolowsky)
