Two young Orthodox Christians were killed in an attack on a church in southern Ethiopia on Saturday, according to a report by a religious media outlet.

The incident comes against a backdrop of tensions in the ancient Ethiopian Orthodox Tewahedo Church after rebel bishops created their own synod in Oromia, the country's most populous region.

Abune Henok, Archbishop of Addis Ababa Diocese, described the attack in the city of Shashamene as "shameful and heartwrenching", according to the Church-affiliated Tewahedo Media Center (TMC).

It said two people had been killed, and another four had sustained heavy injuries, accusing security forces of carrying out the assault in the Oromia city that lies about 250 kilometres (150 miles) south of Addis Ababa.

It was not possible to independently verify the report.

Abune Henok called on the authorities in Oromia, also the largest geographic region in Ethiopia, to stop the "persecution" of Orthodox Christians, according to the TMC.

The unity of the Church, one of the oldest in the world and which accounts for about 40 per cent of Ethiopia's 115 million population, is under threat after the move by the rebel clergy last month.

The Church, headed by Patriarch Abune Mathias for a decade, has declared the breakaway synod illegal and excommunicated the bishops involved.

It has also accused the government of Prime Minister Abiy Ahmed of interfering in its affairs and making comments that effectively recognised the "illegitimate group".

Addressing cabinet members earlier in the week, Abiy -- who is himself from the Oromo community -- called for the rivals to engage in dialogue and said both sides had their "own truths".

The breakaway bishops accuse the Church of discrimination and linguistic and cultural hegemony, saying congregations in Oromia are not served in their native language, claims rejected by the Patriarchate.

Orthodox leaders have long complained of religious persecution, including the burning of churches several years ago, and relations with the government have been tense in the past, including over the Tigray conflict.

The World Council of Churches on Friday issued a statement voicing "deep concern" about the developments in the Ethiopian institution.

"We call upon all political leaders in Ethiopia to support the Ethiopian Orthodox Tewahedo Church in its efforts to achieve unity and peace among its members," WCC general secretary Jerry Pillay said.