Papua New Guinea Prime Minister James Marape had confirmed his government will finalise up to nine agreements with Jakarta to strengthen its relationship with Indonesia.

He was expected to discuss a proposed partnership with the Indonesian Petroleum company - Pertamina - for alternative sources of fuel among a number of issues on the agenda during the visit which ends on Friday.

Marape said the Memorandum of Understanding signed between the two countries "will greatly complement Papua New Guinea's future socio-economic agenda and reap tangible outcomes in the immediate to long term."

But PNG Think Tank Group executive director Samson Komati said Marape had his priorities mixed up.

"We have all these problems here in the nation and you have the Prime Minister leading a delegation like this when our house is not in order, he is going overseas. It is a very wasteful exercise I think," Komati said.

Komati said government departments were struggling to carry out their core functions because money allocated to them by the state had not reached them.