Kiir told UN Security Council delegation in Juba that Beshir is wilfully stalling the vote.
The delegation then flew to El Fasher in Darfur, where hundreds of Beshir supporters protested against International Criminal Court’s genocide charges against Sudanese leader.
"With our blood, with our soul we sacrifice for Beshir!" they shouted as they blocked the exit of the airport, briefly preventing the delegation from leaving.
Representatives from the 15 nations on the UN Security Council, including the five permanent powers – Britain, China, France, Russia and the United States – are on a four-day mission to Sudan to inspect preparations for next year’s referendum on southern independence and to visit Darfur.
"We are concerned about sexual violence, we are concerned about child soldiers, we are concerned about the import of weapons into the region," said Britain's ambassador, Mark Lyall Grant.
John Andruga Duku, who heads the International Countdown to the Southern Sudan Referendum, told RFI that the government is intimidating people in the south to put them off voting for independence.
The ambassadors will visit one of the Darfur refugee camps on Friday before going to Khartoum for the final leg of their mission. They are not meeting Bashir because of the charges against him. They will meet Sudan's foreign minister before leaving on Saturday.
Bashir is flying to Libya on Friday to attend Arab League and Arab-African meetings over the weekend.
Sudanese forces were conducting a manhunt in El Fasher on Friday after gunmen kidnapped a UN staffer during a visit by Security Council ambassadors.
It is the first civilian abduction in the city, although there have been other security concerns.
"Sudanese police have stepped up security at checkpoints in all El Fasher," spokesperson Kemal Saiki said.
He said four or five gunmen broke into a house where UN staff were based at nightfall on Thursday and abducted two of the four people in the building at the time. They tied them up and took them away in one of the Unamid cars that was there, but one escaped by jumping out of the car.
It is unclear who is responsible for the kidnapping. Britain's UN ambassador Grant said he did not think the abduction was linked to their presence.