Hideto Kijima, 44, was returning last month to Osaka from a vacation in Amami, a small island off southern Japan, when a Vanilla Air employee told him that company safety rules banned anyone from carrying him up the stairs.
There was no lift at the small airport to move disabled passengers from the tarmac up to the jet's door.
Mr Kijima, who is paralysed from the waist down, said in a blog he was forced to crawl up the stairs using only his arms.
The Asahi newspaper said the man pulled himself up some 17 steps.
Vanilla Air, the budget arm of major carrier All Nippon Airways, said on Wednesday it has apologised to Mr Kijima.
The airline had previously barred passengers who could not walk from boarding a flight at Amami because it was dangerous to carry someone up the stairs, the spokesman said.
Mr Kijima, a frequent traveller outside Japan, told Nippon TV on Wednesday he was "surprised" when staff said he would not be able to fly if he could not walk up the stairs.
"I wondered if the airport employees didn't think that was wrong," he added.
The incident comes after a public relations fiasco on United Airlines in April, in which a 69-year-old doctor in the United States was dragged off an overbooked flight.
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.