The source said Ajavon is alleged to have committed “forgery of official records, complicity in forgery of official records, falsification and fraud”.
The alleged offences date back to 2009 and could see him jailed if charged and convicted, the source added.
Ajavon, who is known in Benin as “the chicken king”, made his fortune in the agricultural feeds business and has faced a string of legal troubles in recent years.
In October 2016, he was arrested after 18 kilograms (40 pounds) of cocaine with a street value of $16 million was found in a container destined for one of his businesses.
He was released after eight days and subsequently said he had been the victim of a plot to discredit him. Charges were dropped several months later.
In August this year, he was ordered to pay 167 billion CFA francs $300,000) after claims of tax evasion at several of his companies in 2014, 2015 and 2016.
Last Friday, he was in court to respond to allegations that he allowed vegetable oil and frozen chicken to be exported to neighbouring Nigeria, in breach of a trade agreement.
A former ambassador of Benin to Nigeria is one of his two co-accused.
Ajavon’s spokesman said the businessman preferred to let proceedings in court run their course and not to engage in a “media trial”.
Privately, members of Ajavon’s entourage described the allegations as “premature”, without elaborating.
Ajavon stood for election in last year’s presidential election that was won by another businessman-turned-politician Patrice Talon.
He came third, with prime minister Lionel Zinsou in second.
Ajavon won almost a quarter of the first-round vote and supported Talon in his run-off with Zinsou.
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