The New York-based HRW said in a report that rising hostility from the government was making it difficult for civil society groups to freely conduct their work.
President Yoweri Museveni, widely expected to seek a fifth term in office in 2016, has often criticised non-governmental organisations, accusing them of sabotaging government projects and representing the interests of foreign governments.
A government spokesperson rejected the HRW accusations.
HRW cited closure of meetings, reprimands, demands for apologies or retractions, threats, harassment and physical violence as some to the tactics officials have used to obstruct the work of civil society groups.
"Civil society actors working on governance, human rights, land, oil, and other sensitive issues are the main targets of these attacks, apparently because they are viewed as threatening to undermine the regime’s political and financial interests," HRW said.
The east African country discovered commercial crude oil deposits in the Lake Albert region in its west along the border with the Democratic Republic of Congo (DRC) in 2006 and the ministry of energy estimates reserves at 2.5 billion barrels.
UK explorer Tullow Oil says first oil from its Uganda project is still more than three years away.
Fred Opolot, executive director of Uganda government’s media centre, said HRW’s accusations were unfounded.
"I have not read the report but their accusations are utterly false and unfounded. Uganda has an open door policy for civil society as long as they do the right things," he said.
"We don’t stand in the way of any NGO and we have thousands of NGOs doing their work. Some of these outrageous reports serve a purpose, HRW wants to justify its budgets to its donors."
In May Uganda accused British charity Oxfam of bringing disrepute to Museveni after it published a report detailing extensive land grabs by the government in alliance with a foreign company.
The government threatened to eject the charity from the country unless it retracted its accusations and apologised.
The report said for instance, researchers from groups seeking to visit regions with oil deposits were required to seek permission from the Ministry of Energy, a condition HRW said was unlawful and impeded their access to local communities that could be harmed by oil production activity.
The report also said groups promoting gay and lesbian rights were being forced to work underground because criminalisation of homosexuality in Uganda prevented them from registering with the authorities and functioning legally.
An anti-gay legislation which advocated for death penalty for some offenders and first introduced in Uganda’s parliament in 2009 provoked fierce international condemnation and has pitted conservative religious groups in Uganda against donors.