Opposition candidates were harassed by security forces, the media was suppressed by the government, and observers' offices were raided, said the EU Council of Ministers in a statement on Wednesday.
It called on all parties to refrain from violence and for "election challenges and complaints to be addressed in an independent and transparent manner."
Uganda's longtime leader President Yoweri Museveni was declared the winner for a record sixth term, amid an internet blackout and allegations of abuse.
Wine -- a singer-turned-politician, whose real name is Robert Kyagulanyi -- has been under house arrest after the military surrounded his home on Friday. He maintains the election was rigged.
"I thank all friends in Uganda and abroad who continue to stand with us until we put an end to this indignity," he said in a tweet on Thursday.
The 18-month old niece of Wine's wife, Barbara Itungo Kyagulanyi, is in the residence and her father has been denied access because nobody is allowed to leave or come into the compound, Wine said on Twitter.
Human rights groups spoke out against Wine's detention and the political climate in the country as President Museveni embarked on an election victory tour of the country Thursday.
"It is neither a crime to stand for president nor to want to challenge the election results in court," said the regional director of the human rights NGO, Deprose Muchena, in a statement.
"This continued confinement is politically motivated and a blatant violation of their human rights. It must be lifted immediately and without any conditions."
In the weeks leading up to the election, there were several incidences of violence and human rights violations said Human Rights Watch.
"The abuses included killings by security forces, arrests and beatings of opposition supporters and journalists, disruption of opposition rallies, and a shutdown of the internet," said the international human rights NGO in a statement.
