Mr Ekpa, based in Finland, has been accused of fuelling insecurity in South-east Nigeria.
The Chief of Defence Staff, Christopher Musa, has accused the Finnish government and the European Union of shielding Simon Ekpa, a controversial Biafra agitator.
The alleged cover has enabled Mr Ekpa to continue to incite, through social media, violence in Nigeria's South-east state, Mr Musa said.
Mr Musa, a major general, spoke on Wednesday during Channels TV's special broadcast to mark Nigeria's 25 years of democratic governance.
Mr Ekpa, a factional leader of the Indigenous People of Biafra (IPOB), is a dual citizen of Nigeria and Finland.
The Biafra agitator, who is based in Finland, has been accused of fuelling insecurity in south-east Nigeria.
He has continued to issue sit-at-home orders in the region, during which defaulting residents are usually killed or attacked by gunmen enforcing the illegal order.
The Nigerian government had indicated its intention to extradite Mr Ekpa to Nigeria to face prosecution. Still, the plan has not seen the light of the day.
'Finnish govt is supporting him'
Speaking during the programme on Channels TV, Mr Musa said the Finnish government appears to be supporting the Biafra agitator in his alleged terrorist activities in the South-east.
"We have repeatedly complained about the issue of Simon Ekpa. He is in Finland, and the Finnish government is giving him all the support, and he is doing what he is doing," he said.
The chief of defence staff called on the Nigerian government to arrest and prosecute Mr Ekpa for his alleged roles in the worsening insecurity in the country's South-east.
"We have said that in clear terms. We need to diplomatically find a means of getting him out of whatever it is that he is doing. He must be arrested, (and) he must be prosecuted," he said.
Suspicious silence
Mr Musa said the silence of the European Union was suspicious considering the security threats posed by Mr Ekpa in the South-east.
"This is democracy. If the European Union is supporting democracy and this is happening and they are not taking action, then they don't mean well for Nigeria.
"Look at it from the other way. Assuming he (Ekpa) is in Nigeria, he is doing that to the Finnish government, do you think the European Union will allow that to happen? They definitely will not. So why are they allowing him to do what he's doing?" he said.
'People are being killed'
Mr Musa suggested that the arrest of Mr Ekpa has become imperative given that his utterances on social media were leading to further attacks and killings in the region.
As a result of Mr Ekpa's comments on social media, Mr Musa said, "People are being killed and nothing is being done."
The chief of defence staff asked the Nigerian government to take decisive action, including exploring diplomatic options to stop the Biafra agitator.
'What we're doing to stop Simon Ekpa'
Mr Musa said the military has been working with the Central Bank of Nigeria (CBN) and Nigerian Financial Intelligence Unit (NFIU) to stop those sending funds from outside Nigeria to sponsor insecurity in the South-east.
"Stopping the funds is very critical. I know the CBN and the NFIU are doing a lot in tracking down how the funds flow. And this is part of what we call the oxygen of terrorism," he said.
The chief of defence staff noted that a lack of political will was affecting the fight against terrorism in Nigeria.
He called on the state governments to join hands with the federal government to fight terrorism and other forms of criminality in the country.
'Action must follow legislation'
The Finnish Ambassador to Nigeria, Leena Pylvanainen, did not respond to calls and text messages seeking her comments on Thursday.
However, in February 2023, Nigeria's Ministry of Foreign Affairs summoned Mrs Pylvanainen over a threat by Mr Ekpa to disrupt the Nigerian 2023 general elections.
Geoffrey Onyeama, Nigeria's then-Minister of Foreign Affairs, had in the meeting with the Finnish ambassador, asked for the cooperation of the Finnish government to arrest Mr Ekpa's threats to disrupt the exercise.
However, Mrs Pylvanainen said that although the Finnish government was concerned about the situation, there was a need to, consider Mr Ekpa's rights given that he is a Finnish citizen.
"So, everything has to obviously be done according to Finnish legislation," she stated.