The admissions by Toshiba and Sumitomo Mitsui Trust Bank are likely to deepen concerns about corporate governance in Japan at a time of new political leadership and increased scrutiny by investors.
Toshiba said that 1,139 voting forms, representing a combined 1.3% stake, were left out for its annual meeting even though they were delivered before the July 30 deadline to Sumitomo Mitsui Trust, its shareholder registry administrator.
The trust bank said those forms were not counted because they arrived a day before the appointed "delivery date", which led to them being omitted from the tally.
Sumitomo Mitsui Trust said it would review its procedures, but the vote-counting problem may have happened at other clients, because it uses the same vote-counting procedure.
An official of the bank told reporters at an online briefing it would investigate the handling of vote counting for about 970 listed companies that entrusted the bank with such tasks for this year's shareholder meetings.
Toshiba said it would continue its investigation and take appropriate measures, adding that the results of the annual meeting would not change even if all the uncounted votes were tallied.
Separately, the trust banking arm of Mizuho Financial Group Inc said on Friday it would investigate the adequacy of its vote-counting procedure, which is done by a joint venture with Sumitomo Mitsui Trust. The probe will cover more than 400 clients, a spokesman said.
Reuters last month reported Singapore-based hedge fund 3D Investment Partners, a major investor in Toshiba, had called for a third-party investigation into the meeting, saying its vote had not been fully recognised.
A Toshiba executive on Friday confirmed that about 1,300 voting forms with postmarks indicating they were accepted at post offices close to senders on July 27 had failed to be counted for the July 31 meeting.
(Reporting by Makiko Yamazaki and Takashi Umekawa; editing by Chang-Ran Kim, Jason Neely and Simon Cameron-Moore)
By Makiko Yamazaki and Takashi Umekawa