The low-cost notebook computer is aimed at developing nations and supports Linux and Windows operating systems.
Mandriva won the Nigerian contract and started shipping its software for the first 17,000 units. But the firm soon found out that Microsoft's sales team had continued to keep pushing for a deal.
"Today, we hear from the customer a totally different story," Bancilhon complained in an open letter to Microsoft chief executive Steve Ballmer posted on a company blog on Wednesday.
"The customer will pay for the Mandriva Software as agreed, but will replace it with Windows afterwards."
Bancilhon went on to allege that Microsoft used unscrupulous business tactics, apparently claiming that the software giant had allegedly bribed officials.
"What have you done for these guys to change their mind like this? It is pretty clear to me, and it will be clear to everyone," the letter states.
"How do you call what you just did Steve, in the place where you live? In my place, they give it various names, I'm sure you know them.
"Of course, I will keep fighting this one and the next one, and the next one. You have the money, the power, and maybe we have a different sense of ethics, but I believe that hard work, good technology and ethics can win too."
Microsoft denied any wrongdoing, arguing that Nigeria had changed its mind because Windows better matched its needs.
"Microsoft strongly believes that individuals, governments and other organisations should be free to use the software and other technologies that best meet their needs," the company said in an emailed statement.
"We believe Microsoft offers the best overall option of value, integration, interoperability and support, without complexity or added dependency on services.
"Microsoft has a strong relationship with the government in Nigeria and will continue to partner with government and industry to help meet their needs.
"Microsoft operates its business in accordance with the laws of the countries in which it operates and with international law."
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