Cycling’s governing body missed the 28 July deadline and only sent its application to the International Paralympic Committee last week.
“[It] sums up how high we appear on the UCI radar. Not surprised at all,”tweeted British rider Jody Cundy.
The IPC has announced 16 of the maximum of 23 sports for the 2020 Paralympics.
Para-badminton has been included and will makes its Games debut in Japan.
The other sports included are athletics, archery, boccia, equestrian, goalball, powerlifting, rowing, shooting, sitting volleyball, swimming, table tennis, triathlon, wheelchair basketball, wheelchair rugby and wheelchair tennis.
Para-cycling is one of eight sports left chasing up to seven places with the final line-up to be confirmed early next year.
All of the 24 sports seeking to be part of the Tokyo programme had been required to submit their application for assessment by the IPC’s management team by 28 July.
They include the 20 sports which took part in London, Para-canoeing and Para-triathlon, which will make their debuts in Rio in 2016, as well as Para-badminton and Para-taekwondo, who were bidding to be included for the first time,
Their recommendations were discussed by the IPC Governing Board on Tuesday at a meeting in Berlin.
Cycling’s late application meant it could not be assessed in time for the meeting in Berlin, to the disappointment of the the IPC and the frustration of the riders.
“How as riders can we have faith in the UCI, when they can’t even submit an application to be in the Tokyo Paralympics on time,” added Cundy.
The remaining eight sports will now have to present additional information to the IPC addressing the issues identified in their applications and a further meeting will be held in Abu Dhabi on 30 January and 1 February.
“Our aim is to ensure that the final Tokyo 2020 Paralympic sports programme is fresh and features the best Para-sports possible,” said IPC president Sir Philip Craven.
“Although we can have a maximum of 23 sports in six years’ time, we have an option to reduce the number of sports in order to ensure we have a compelling and attractive Para-sports programme.”
In a statement, the UCI say they will work closely with the IPC ahead of the meeting in Abu Dhabi
It went on: “The UCI remains fully committed to the promotion of para-cycling and looks forward to a positive dialogue with the IPC over the next few months to ensure that cycling continues to play its part in helping the Paralympic Games go from strength to strength.”
The Tokyo Games will be held from from 25 August to 6 September 2020.
Great Britain has been one of the most successful Para-cycling nations since the sport made its Games debut in Seoul in 1988.
They topped the sport’s medal table in Beijing in 2008 and also at London 2012 where they won 22 medals, including eight golds, in front of huge crowds at the Velodrome and Brands Hatch, where the road events took place.
The team’s success continued this year with 18 medals, including 10 golds, in this year’s Road and Track World Championships with Dame Sarah Storey winning gold medals at both events to follow up her four Paralympic golds in London.
A British Cycling spokesperson said: “It is disappointing news but Para-cycling was one of the big successes of London 2012 and we are confident the UCI and the IPC will act to ensure the sport retains its place on the Paralympic programme.”