Binance's regional manager for Africa, British-Kenyan Nadeem Anjarwalla, was detained alongside colleague Tigran Gambaryan by the Nigerian government in late February.
While the two executives were not charged with any crime, the government demanded almost $10 billion in compensation from the cryptocurrency firm, accusing it of manipulated foreign exchange rates through currency speculation and rate-fixing.
The central bank governor Olayemi Cardoso said Binance Nigeria had moved $26 billion worth of untraceable funds.
A presidential spokesman has now told Bloomberg that Anjarwalla has escaped from the guest house where he was being detained. Amid speculation that he has fled the country, Nigerian is working with Interpol to secure an international arrest warrant for him.
A Binanance spokesperson has told CNBC: "We were made aware that Nadeem is no longer in Nigerian custody.
Our primary focus remains on the safety of our employees and we are working collaboratively with Nigerian authorities to quickly resolve this issue."
Separately, Nigeria has laid new allegations against Binance and the two executives. The Federal Inland Revenue Service (FIRS) has announced multiple charges, including failure to pay VAT and Company Income Tax, and enabling tax evasion through its platform.