Human Rights Watch said the 43 men and teenaged boys were taken in police sweeps of Uighur districts of Urumqi, and had since vanished without a trace.
The riots and protests in the city in early July left nearly 200 people dead.
China's central government declined to answer questions about those detained by the authorities in Xinjiang.
It referred questions about the ethnic unrest to the regional government, which also did not respond to enquiries from the BBC.
"The cases we documented are likely just the tip of the iceberg," said Brad Adams, Asia director at Human Rights Watch.
The rights group is calling for the Chinese government to give details of everyone it is holding in detention.
In a report on the disappeared people, HRW said the police had searched two Uighur areas of Urumqi immediately after the riots. At least 43 people were taken away and had not been heard of since.
"According to witnesses, the security forces sealed off entire neighbourhoods, searching for young Uighur men," the group said.
HRW said most of those taken away were young Uighur men in their 20s. The youngest are reported to have been 12 and 14.
In many cases, families had been unable to find out what had happened to their relatives, said Human Rights Watch, whose report was based on interviews with local people.
"China should only use official places of detention so that everyone being held can contact family members and legal counsel," said Mr Adams.
"Disappearing people is not the behaviour of countries aspiring to global leadership."
Ethnic Uighurs, the original inhabitants of Xinjiang, went on the rampage after reports of Uighur deaths in southern China.
They mainly targeted Urumqi's Han Chinese community - a group that has moved into the western region more recently - killing scores of people.
Uighurs say their culture has been undermined since the arrival of millions of Han people from other parts of China.
Two months after the riots by Uighurs, Hans staged their own protests.
Afterwards, a confused picture emerged about exactly how many people had been arrested, partly due to a reluctance by the authorities to provide detailed figures.
At one point the authorities said more than 1,500 people were in detention, but so far only a handful have been prosecuted.
The first trials began last week. A total of nine people have been sentenced to death for their involvement in the riots.
Critics say the trials do not meet international standards.