Kizza Besigye was detained during a raid on his party's headquarters in the capital, Kampala, following Thursday's tightly contested elections. Police also fired tear gas, as clashes broke out with his supporters.
With official results for nearly half of the polling stations declared, President Yoweri Museveni is leading.
He is running for a fifth term, after 30 years in power.
This is the third time in the space of a week that Mr Besigye has been detained.
He was released on the two previous occasions without being charged.
His latest arrest came as he was about to hold a press conference.
The US embassy in Uganda condemned the crackdown in a post on its Twitter account.
After
Mr Besigye was briefly detained on Thursday, the US State
Departmentsaid the arrest called into question "Uganda's commitment to a
transparent and free election process".
It also criticised a temporary shutdown of social media, chat apps and mobile money services.
President Museveni said the decision had been taken for security reasons, and to prevent people from "telling lies".
Police raided the opposition headquarters ahead of a planned press conference
There
is a heavy deployment of police and soldiers in neighbourhoods around
the headquarters of Mr Besigye's Forum for Democratic Change (FDC)
party, reports the BBC's Catherine Byaruhanga from Kampala.
President
Museveni currently leads with 62% of the vote, while Mr Beisgye has
33%, according to provisional results released by the electoral
commission.
Voting is still taking place in a handful of places
where the late arrival of election materials meant that polling stations
did not open on Thursday.
Commonwealth election observer
mission head, Nigeria's former President Olusegun Obasanjo, condemned
the failure of voting stations to open on time.
"Delays of three,
four, five and even six hours, especially in Kampala, are absolutely
inexcusable and will not inspire trust and confidence in the system and
the process," he said.
A candidate needs to secure more than 50% of the vote to avoid a run-off with the second-ranked contender.
Ugandans also voted in parliamentary and local elections.
Final results are expected by Saturday.
Voting at some polling stations was extended into a second day after delays
Commonwealth election observer mission head, Nigeria's
former President Olusegun Obasanjo, condemned the failure of voting
stations to open on time.
"Delays of three, four, five and even
six hours, especially in Kampala, are absolutely inexcusable and will
not inspire trust and confidence in the system and the process," he
said.
A candidate needs to secure more than 50% of the vote to avoid a run-off with the second-ranked contender.
Ugandans also voted in parliamentary and local elections.
Final results are expected by Saturday.
Major presidential contenders:
- Kizza
Besigye, 59, veteran opposition leader and once personal doctor to
incumbent President Museveni. He has lost the last three elections
- Amama
Mbabazi, 67, former ally of President Museveni and once prime minister
and also served as defence, security and justice ministers
- Yoweri
Museveni, 71, in power since winning a five-year guerrilla war in 1986
and he is one of Africa's longest-serving leaders. His final term was
meant to end in 2006, but in 2005 he won a campaign to lift the
constitutional term limits.
Dhaqaatiirta ayaa ku taliyay in ay baaritaan dheeri ah ku sameeyaan ninkaan oo markii hore da’diisa lagu sheegay 15-sano jir balse isbuucii hore ay Laanta Socdaalka sheegtay in uu ka weynyahay 18-sano. Haddii baaritaanka ugu dambeeya uu muujiyo in uu waalanyahay wiilkaan ayaa dhaqaatiirtu waxay ku talin doonaan in la geeyo xanaanada dadka waalan ama maanakoobiyo oo aan xabsi la dhigin.
Wiilkaan ayaa middi ku dilay gabar u dhalatay wadanka Lebanon oo 22-sano jir ah taasoo ka mid ahayd shaqaalaha guriga uu ku noolaa.
Dilka uu geystay wiilkaan ayaa argagax weyn ku dhaliyay Swedishka, iyadoo markii hore la sheegay in madaxa looga jiro balse dambi oogaha ayaa sheegtay in ay wali baaritaan ku hayaan wiilkaan oo aysan sheegi karin in uu xanuunsanyahay iyo in kale.
Somaliska
Uganda polls: Museveni's main rival, Besigye, arrested
Kizza Besigye was detained during a raid on his party's headquarters in the capital, Kampala, following Thursday's tightly contested elections.