He said the Niger Delta region will not take kindly to Jonathan's arrest.
In a recent interview with Independent, Orubebe said arresting the former president will lead to heightened tension in the Niger Delta region where he comes from as it will be seen as victimisation by the current administration.
He further argued that the only justification to arrest Jonathan would be if past Presidents and Heads of State are investigated for their own past conducts.
He said, "I vehemently say that for them to make any mistake of arresting Jonathan will not augur well for the present government. But we know that past Presidents and Heads of State in the country have committed a lot of atrocities against this country and nobody raised an eyebrow.
"I repeat if Buhari's government makes any attempt to arrest President Jonathan, it will not be taken kindly particularly by the Ijaws. In fact, the country will burn.
"I know for sure that Buhari's government will not arrest Jonathan. So, let's leave it like that. But in case it happens, the entire Niger Delta will boil and Buhari will not be comfortable wherever he is. In fact, government should not think of that.
"Although Jonathan ignored his people when he was in power and developed the North, be that as it may, let this government remember that he came from somewhere because he remains our son no matter what.
"If the government wants to make any arrest, they should start from the past Presidents and Heads of State that did something unconstitutional against this country.
"I remember that Chief Obasanjo's name was mentioned in the Halliburton scandal; so, they should not think of arresting Dr. Jonathan because it will backfire seriously on them."
Orubebe also advised the former president to make efforts to resolve issues with the current administration in private rather than the public domain.
He said, "On the other hand, Dr. Jonathan should also keep to the golden rule of silence. He should quietly call on President Buhari and discuss issues with him because I have never seen former a president castigating the incumbent president.
"Even Chief Olusegun Obasanjo, who is very outspoken, keeps to that rule. He visits President Buhari and iron out issues with him. So, Jonathan should emulate Obasanjo and maintain the golden rule of silent as a former president."
Former president jonathan has been in the news lately as he has been invited to testify as a defence witness in the money laundering trial of former National Publicity Secretary of the People's Democratic Party (PDP), Chief Olisa Metuh.
He has also been dragged into the corruption scandal involving former chairman of the defunct Presidential Task Team on Pension Reforms (PTTPR), Abdulrasheed Maina, who allegedly committed a N2 billion pension fraud.