Organisers say the duo are from the same team and sport as the official who tested positive on Saturday.
Other members of the team are being isolated in their rooms.
The pair are the first athletes to test positive in the village, although a further athlete also tested positive on Sunday elsewhere.
In total, organisers on Sunday reported 10 new cases connected to the Olympics including media, contractors and other personnel. That compares with 15 new cases on Saturday.
Infection rates are rising among the general population of Tokyo, topping 1,000 new cases for four consecutive days. Polls show many Japanese people oppose holding the Games with the influx of overseas visitors it entails.
Tokyo 2020 spokesman Masa Takaya said the three cases “were from the same country and sport”. They are “isolated in their rooms and Tokyo 2020 is delivering meals to them”, he said, adding that the rest of the team – which has not been identified – have also been tested.
Speaking on Saturday, Games chief Seiko Hashimoto said: “Athletes who are coming to Japan are probably very worried. I understand that.
“We are doing everything to prevent any Covid outbreaks. If we end up with an outbreak we will make sure we have a plan in place to respond.”
Australia’s entire athletics team for the Tokyo Olympics were quarantined in their rooms on Saturday at their pre-Games training camp in Cairns, following a Covid-19 scare.
An inconclusive test had been returned by an official but subsequent tests were negative, the Australian Olympic Committee (AOC) confirmed on Sunday.
Athletes have since been permitted to compete in a warm-up event
“My understanding is [Athletics Australia] applied an abundance of caution,” said David Hughes, the AOC’s chief medical officer.