The four were detained at Entebbe Airport by immigration officials despite having secured an appointment with the Ugandan Chief Justice over the continued detention of activist Al-Amin Kimathi.
Mr Omar said they had been made to sign deportation documents and they were waiting to catch a flight to Nairobi.
Hussein Khalif of the Supreme Council of Kenya Muslims, Sheikh Muhdhar and Mr Sam Muhoji had accompanied Mr Omar to the neighbouring country.
However, six other human rights campaigners and lawyers were allowed entry.
Speaking to the Nation by telephone, Mr Omar said they arrived in Uganda at 9.30 am for a two-day visit.
“We were however denied entry and our passports taken. I have travelled all over the world and nobody has ever stopped me,” Mr Omar said.
The group was to meet Ugandan human rights officials Wednesday before honouring their date with the CJ the following day.
Mr Omar said no reason was given for their detention and denial of entry since had they met all traveling requirements.
“Everything is in order. Kenyans do not need visas to come to Uganda,” Mr Omar said.
Activist Al-Amin Kimathi was among eight Kenyans arrested over the July 11 Kampala bombing.
Seventy four people were killed and many injured in the attack on a club where fans were watching the final of the World Cup.
Mr Kimathi, the executive co-ordinator of Muslim Human Rights Forum, was arrested in Kampala when he went to visit Kenyan youth handed to Uganda by the Kenya police
Ugandan authorities allege that seven of the suspects were recruits of al-Shabaab who had returned from Somalia to execute their mission.
“Al-Amin Kimathi provided money to Mohammed Ali, who is still at large, to rent safe houses in Nairobi, which were used as a base for the mission and house the suicide bombers, one house in Kawangware and another in South B,” the charge sheet reads.