Oando's share price was frozen at 5.99 naira on Monday until further notice, the stock exchange said after the Securities and Exchange Commission (SEC) ordered the audit.
The SEC suspended trading in the stock for 48 hours last week, saying it was investigating complaints about insider trading and discrepancies in its ownership structure.
"The actions taken by the SEC, the suspension of the shares of the company and the initiation of a forensic audit, are prejudicial to the company," an Oando spokesman told Reuters.
The Nigerian Stock Exchange said it was reviewing the court processes to provide an appropriate defence against the court order. The SEC declined to comment, saying that it was yet to receive the court order.
By 1236 GMT, only 42,923 shares at the firm's fixed share price of 5.99 had traded. The company recorded no trades on Monday. A regulatory source said the freeze aimed to avoid volatile trading pending the outcome of the audit.
In an SEC letter to Oando dated Oct. 17 the regulator accused Oando of corporate governance abuses and financial mismanagement, basing its allegations on two petitions received from Dahiru Barau Mangal and Ansbury Incorporated.
It added that it would engage accountancy firm Deloitte to lead the audit together with lawyers and stockbrokers, at a cost of 160 million naira, which would be borne by Oando.
A company source has said the petitions centred on the ownership of some Oando shares bought through an investment vehicle at the time the company acquired the Nigerian subsidiary of US oil company ConocoPhillips for $1.65 billion in 2014.
Oando has said it was aware that the regulator had received petitions but the allegations were "unsubstantiated, misleading and defamatory".
However, it had not received any notification from the regulator querying its compliance until the recent letter, adding that it has been cooperating with the SEC since the start of its investigation in May.
In July Oando's share price fell close to a one-month low after the regulator said it was investigating the firm's shareholding structure following the ConocoPhillips acquisition.
Trading in Oando's shares have also been suspended in Johannesburg, where it has a secondary listing.
Oando's share price has gained 27 percent this year after a sharp fall last year.