The video was shot at a national park on the island of Java. Researchers used "movement-triggered" hidden cameras.
Javan rhinos are one of the world's most endangered species, with an estimated population of no more than 50 in Indonesia's Ujung Kulon National Park. A few others live in Vietnam's Cat Tien National Park.
"This is good news to ensure that the population is viable," said Adhi Hariyadi, WWF project leader in the park.
Several videos caught the rhinos last November and December. The footage showed two mother Javan rhinos and two calves. One of the calves is female, indicating the rhinos are still viable.
"This female calf documentation is a breath of fresh air for us - and Javan rhino conservation in general - since majority of calves we identified previously was male," said Hariyadi.
Over the past 50 years poaching has largely contributed to the decimation of rhino numbers in Indonesia. Their horns are used in traditional Chinese medicines.
The Associated Press contributed to this story