"There should be no prejudice. There are laws to protect shareholders," Atsushi Saito told a regular news conference.
Olympus, he added, should avoid picking members of a panel it has promised will investigate its M&A activity who lean toward the management's position.
Olympus agreed on October 21 to appoint the third-party panel to look into the deals, although it has yet to identify its members. Saito said he suggested on October 14 that it establish such a group.
Executives at Olympus are struggling to convince shareholders it acted properly in paying a record $687 million in advisory fees to two obscure firms related to the $2 billion acquisition of British medical equipment maker Gyrus in 2008. They are also under fire for the purchase of three companies in Japan, the values of which it has since largely written down.
Saito described the scandal and management decision that had spurred a sharp drop in the firm's corporate value as "very regrettable".
Olympus's shares resumed a slide on Friday, falling 10 percent to 1,217 yen, following a rebound Thursday after Tsuyoshi Kikukawa, the executive at the heart of the furor and architect of the ousting of Olympus's British CEO Michael Woodford two weeks earlier, resigned as chairman and president.
Since the boardroom putsch against Woodford the company's market value has almost halved.
In a bid to curtail margin trading, the Tokyo bourse said later in a release that it was temporarily raising the payment required for such trades, when shares are bought with money borrowed from brokers using other securities as collateral.
The exchange probably wants to cool off overheated Olympus share trades, said Tomoichiro Kubota, an analyst at Matsui Securities
Kikukawa's successor, Shuichi Takayama, on Thursday defended the 92-year-old company's payments to financial advisers, which the ousted Briton has identified as New York-based AXES America LLC and Cayman Island-based AXAM Investment Ltd.
That fee amounted to 36 percent of Gyrus's acquisition price. Fees to advisers in M&A deals typically amount to no more than 2 percent.
Takayama also insisted that Olympus had acted properly when it paid $773 million for three domestic firms -- a microwave cookware maker, a medical waste recycler and a cosmetics firm that together employ around 120 people.
Olympus revealed on Friday that combined revenue for the three businesses will likely amount to 6.5 billion yen ($86 million) this business year, less than a tenth of an estimate it made in 2008 for sales of 88.5 billion yen in the 12 months to March 31, 2013.
Woodford, who provided internal documents to Reuters and other media outlets related to those deals and the Gyrus acquisition following his firing, said on Wednesday he is in contact with the FBI about the scandal.
Olympus said it is unaware of any probe by the U.S. Federal Bureau of Investigation into payments it made to the financial adviser.
"Some media have reported that we have been contacted by the FBI. So far we haven't confirmed that," it said in a statement.
A Japanese market watchdog, the Securities and Exchange Surveillance Commission, is also looking into the company, sources familiar with the matter told Reuters.
Saito's call on Friday for a thorough investigation comes after Masaki Shizuka, the senior executive officer overseeing listings at the exchange, told a parliamentary committee on Thursday that there were concerns investors might lose trust in information provided by Olympus because the management was in place at the time of the deals in question.
($1 = 75.840 Japanese Yen)
(With additional reporting by Daiki Iga and Nobuhiro Kubo; Editing by Chris Gallagher and Michael Watson)