The docking had to be carried out manually because of unspecified malfunctions in the navigation system, said Vladimir Solovyov, flight director of the Russian segment of the ISS.
A special commission was expected to report by Tuesday on the cause of the malfunctions, Solovyov said.
The Progress M-21M space freighter was loaded with almost 2.5 metric tons of food, fuel, experiment hardware and other supplies for the space station's six Expedition 38 crew members. The craft lifted off aboard a Soyuz-U launch vehicle from the Russian-leased Baikonur space center in Kazakhstan on Tuesday.
On November 28, the spacecraft conducted flybys of the orbital station and successfully tested a lighter and more efficient automated navigation and docking system, known as Kurs-NA.
The Kurs-NA boasts advanced electronics, a fully-digitized control system and increased docking precision compared to its predecessor, Kurs. The improved system will be used on all upgraded Soyuz and Progress vehicles in the future.
The space station's crew currently comprises Russian cosmonauts Mikhail Tyurin, Sergey Ryazanskiy and Oleg Kotov, NASA astronauts Rick Mastracchio and Mike Hopkins, and Japanese astronaut Koichi Wakata.