Kenya's relationship with Somalia is set to deteriorate further following Thursday's controversial Jubbaland polls that saw Sheikh Ahmed Madobe cruise to victory.

Already, Parliament is considering KDF intervention in the disputed Indian Ocean maritime border, in which Nairobi has accused Modadishu of encroachment.

President Mohammed Farmaajo, through the ministry of interior, rejected Madobe's re-election as president of the state, which is one of most stable regions in Somalia.

"Somali federal government announces it will not recognise results from “self-appointed” elections in Kismayo on Thursday.

"The Federal Govt says process followed was not inline with electoral process set out by the Ministry of Interior, Federal and Reconciliation," said Harun Maruf.

Sheikh Madobe, the commander of Ras Kamboni Brigade, helped Kenya neutralise Al-Shabaab militants in the Southern sector, before liberation of Kismayo.

Already, President Uhuru Kenyatta, through Foreign Affairs department, has lauded Madobe for Thursday's victory. He scored 56 votes of 74 parliamentary polls.

"The government and the people of the republic of Kenya take this opportunity to congratulate President Ahmed Madobe for his re-election as president of Jubbaland, a member state of Somalia.

"Kenya shares with great people of Jubbaland for peaceful electoral process, a demonstration of strong and unwavering will of the people to determine their governance and guarantee their security and political stability," read the statement.

Earlier, pro-opposition Parliament in Jubaland “elected” Abdirashid Mohamed Hiddig as regional leader. Reports say 59 out of 75 MPs voted for Hiddig who is also a member of the federal Parliament of Somalia.