A South African court has granted an interim order to prevent Sudanese President Omar al-Bashir from leaving South Africa, where he is attending an African Union summit, until it hears an application calling for his arrest.

The International Criminal Court (ICC) issued an arrest warrant in 2009, accusing Bashir of war crimes and crimes against humanity related to the conflict in Darfur. He denies the charges.

An application reportedly lodged by a human rights group was set to be heard in the Pretoria High Court at 3pm local time on Sunday to decide whether Bashir should be arrested.

The judge said the court will decide whether a South African government cabinet decision to host Bashir would trump the ICC arrest warrant.

Bashir boarded a flight on Saturday to Johannesburg to head Sudan's delegation at the summit which starts on Sunday, presidential sources and the state Sudan News Agency said.

The South African Broadcasting Corporation reported that Bashir was later "welcomed by South African officials and Sudanese diplomats on his arrival in the country".

South Africa is a member of the ICC, which does not have its own police force and relies on member states to detain suspects.

Since the arrest warrant was issued, most of Bashir's trips abroad have been to non-ICC states such as Saudi Arabia and Egypt.

But he has also been to member states that have declined to arrest him, such as Nigeria, which hosted him in July 2013.

"Allowing President al-Bashir into South Africa without arresting him would be a major stain on South Africa's reputation on promoting justice for grave crimes," Elise Keppler, acting international justice director at New-York based advocacy group Human Rights Watch, said in a statement on Friday.

A South African government spokesperson declined to comment.

Bashir cancelled a trip to Indonesia for a summit in April at the last minute. The plan to attend an Asian-African leaders conference in Jakarta sparked protests among rights groups, who want the president to be arrested.

Al Jazeera's Fahmida Miller, reporting from Johannesburg, said an increasing number of African countries have been displeased with the ICC and want to move away from it.

Read more: Africans push UN to call off 'racist' court

"The chances that South Africa will act on the ICC's request are very low. However, it is in an awkward position as it is a signatory to the Rome Statute, which established the ICC," she said.

"At the same time, an arrest by South Africa, any possibility of it, may further tarnish the image of South Africa in the African Union.

"In recent months, a sentiment within the African Union has been growing against the ICC, especially after Kenyan Vice President William Ruto's and Kenyan President Uhuru Kenyatta's appearances at the court."

Burundi crisis

Leaders meet in Johannesburg on Sunday for an African Union summit which will be dominated by the political unrest in Burundi and the migration crisis in the continent.

Burundi has been plunged into a period of instability caused by President Pierre Nkurunziza's push to run for a third five-year term.

Violent protests have left around 40 people dead and 100,000 people have fled the country, raising peace and security concerns in the region.

Other crises like the threat posed by armed groups are also on the agenda in Johannesburg.

"The situation in Burundi is still unresolved ... and Nigeria, which is supposed to be an important player, still has challenges around Boko Haram," said Tjiurimo Hengari, research fellow at the South African Institute of International Affairs.

"I see the next two years being very challenging, especially in light of a new threat that is emerging on the horizon - the issue of constitutional revisions to allow sitting heads of state third terms and fourth terms."