The international development secretary, in Nigeria on a two-day visit, has laid out plans for reviewing the way the UK allocates aid funding.

On her first visit to west Africa as secretary of state, Penny Mordaunt said that, as the UK’s exit from the EU in March 2019 approaches, she wanted to see Nigeria’s relationship with the UK move towards greater trade and investment.

“We want to move from a relationship based on aid to one of economic prosperity and trade,” she said, speaking to the Guardian. “That’s what Brexit is part of. There are really big opportunities here in future years.” According to the Department for International Development (DfID) UK-Nigeria trade was worth £3.4bn in 2016.

A new Human Capital Index announced by the World Bank will come into effect later this year. It ranks how much countries invest in “human capital” such as education and health relative to their wealth and ability to fund those services. The measure was announced by the World Bank’s president, Jim Yong Kim, in April, with Mordant and Bill Gates early supporters.

From next year the index will be used by DfID as a significant part of a formula determining whether UK aid will be reviewed to recipient countries. The new measure could lead to significantly reduced funding for countries like Nigeria that underinvest in health and education.

According to Mordaunt, countries that take on refugee populations will also receive greater aid from the UK. “What the index does is look at what nations can afford to invest in their own people,” she said. “What it will flag up, those nations at the bottom of the index, will be nations that can afford to do this and chose to outsource to the development community. The states [within Nigeria] that DfID has been working with are doing much more on this.”

Nigeria currently spends 4% of its budget on health but in the past year it has increased revenues dedicated to health services. On Friday Mordaunt met the vice-president, Yemi Osinbajo, and said that they had made progress on commitments to increase Nigeria’s investment in health and other social spending.

The UK spends £300m on foreign aid in Nigeria, making it the third largest recipient of British assistance globally after Pakistan and Ethiopia. The budget spent on Africa’s largest economy is seen within the international development ministry as a focal point for reviewing aid. A unit set up in February has worked on improving tax collection in developing countries, reducing dependency on aid further.

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While in Nigeria Mordaunt visited a primary health care facility in Kaduna, northern Nigeria. The Badarawa health centre, which treats more than 22,000 people, is one of many that have received regular medical supplies from DfID since 2014. Kaduna state will take on the costs of medical equipment from this year, beginning a phasing out of UK aid to health centres under an agreement reached with the state. Kaduna increased its allocation on health from 7% of its budget in 2015 to 13% this year.

Mordaunt said: “This has been a real success story in what we’re trying to achieve. What we want to do is to try and move from an aid relationship, making sure that we were being smart about the money we spend. What we want to do is say to the British taxpayer that we have done the most good with the money we have in our budget.

Last year, £100m of UK aid went towards alleviating the humanitarian crisis left in the wake of the Boko Haram terrorist group’s nine-year insurgency in north-eastern Nigeria.

Approximately 1.7 million people remain displaced, with millions still in need of food assistance. President Muhammadu Buhari had pledged to defeat Boko Haram and, despite severely degrading the group from the occupying force it was before his term began in May 2015, it remains a threat, with deadly attacks occurring more frequently in the past few years.

After controversial claims to have defeated Boko Haram made by Buhari’s administration, in the past year the Nigerian army has urged thousands of internally displaced people to return to their homes, promising that their towns have been secured from any terrorist threats. Yet aid groups have raised concerns that towns recently recovered from Boko Haram remain deeply insecure, posing a risk to returnees. Attacks in the past few months in recently opened towns such as Bama have killed dozens.

On Thursday, the aid organisation Médecins Sans Frontières said the humanitarian situation was deteriorating, describing the continuing threat and severe need in towns deemed by the military to be safe. “The reality is that the places they are moving to are not prepared to provide even the most basic services,” said Luiz Eguiluz, the head of MSF’s mission in Nigeria. “The problems in north-east Nigeria are changing instead of being solved.”

Mordaunt said that she wanted to see towns where internally displaced people have returned to fully secured. “There’s no good people returning if security is not in place. What we want to do now is really help move from that humanitarian situation to a recovery and stability programme. You need all players in that, a programme where people who return to those areas return to full security, jobs and livelihoods.”

She stated that humanitarian assistance and training provided to the Nigerian military to defeat the group would continue but her department was encouraging Nigeria to do more to address the humanitarian crisis.