Pope Francis has brushed off security concerns as he arrived in Kenya for his first visit to Africa, a whirlwind tour of three countries that will mark the first time a reigning pontiff has flown into an active armed conflict.

His Alitalia aeroplane arrived at Jomo Kenyatta airport in Nairobi on Wednesday for the first stage of the pope’s visit, which will also take in Uganda and Central African Republic (CAR).

The latter country, which has a majority Christian population, has been in the grip of violence since Muslim rebels seized power in March 2013. More than one in five people have been forced to flee their homes.

When asked if he was concerned about security risks, the pope quipped: “To tell you the truth, the only thing I’m concerned about is the mosquitoes. Did you bring your spray?”

Francis was greeted by President Uhuru Kenyatta and Nairobi’s governor, Evans Kidero, and others amid singing by traditional dance groups.

Speaking before his plane touched down, he said on Wednesday he wanted to offer spiritual and material support to Africans. “I am going with joy to Kenya, Uganda and the brothers of Central African Republic,” he said on the flight. “Let’s hope this trip brings better fruit, both spiritual and material.”

Large crowds held back by hundreds of police gathered along the road from the airport and cheered as the pope’s motorcade passed by.

After greeting Kenyatta, Francis was presented with a bouquet by a boy and a girl. Traditional dancers, some dressed in Maasai regalia, and choirs at the airport sang “karibu baba” in Swahili, lyrics which translate as “welcome father”. Later, Francis was welcomed by an honour guard at the state house and a 21-gun salute.

The pontiff wants to bring a message of peace and reconciliation to parts of Africa torn by extremist violence. Leaders in Africa heeded his message. Kenyan senator, Joy Gwendo, said she hoped the pope’s presence would help bring about the reconciliation of Kenyans divided along tribal lines.

But security concerns are so high that the pope could be forced to make changes to his itinerary for the final leg of the trip. On the eve of Francis’s departure, the Vatican spokesman, Rev Federico Lombardi, insisted there were no new threats and that the pope planned to carry on with his schedule. But in a sign that the Vatican was on alert, Francis’s chief bodyguard made a last-minute visit to CAR’s capital, Bangui, this week to get the latest security updates, and will meet the pope once he lands in Nairobi on Wednesday afternoon.

The bodyguard, Domenico Giani, said upon his departure that “some small modifications” could be made to the itinerary if risks emerged, especially for the civilian population or the UN peacekeeping operation.

Before he arrives in CAR, Francis is expected to discuss issues close to his heart in Kenya and Uganda, including poverty, the environment and the need for interfaith dialogue.

He is also likely to challenge the countries’ political leaders on corruption. Transparency International ranked Kenya 145 of 174 countries in its 2014 corruption perception index, while critics of the Ugandan president, Yoweri Musevni, said official corruption had thrived under his three-decade rule.

Francis is likely to raise the issue during his first meeting on Wednesday with Kenyatta, who declared this week that corruption is a national security threat to east Africa’s largest economy.

While in Kenya, Francis will also deliver an important environmental message at the UN environment programme headquarters on the eve of key climate talks in Paris. He will also visit a Nairobi slum and seek to encourage young Kenyan Christians after the attack by Islamist extremists that left almost 150 people dead at a college of mostly Christian students in April.

In Uganda, Francis will pray at the shrine to the country’s martyrs and celebrate a mass in their honour.

Some uncomfortable issues may also arise: the church’s opposition to condoms as a way to fight Aids, and its support of local legislation criminalising homosexuality are chief among them.

But on the whole, the pope’s visit is meant to tell the African church that it matters, said the Rev Robert Dowd, professor of political science at the University of Notre Dame. “It has a crucial role to play in promoting justice and peace in societies where governments are not always accountable or responsive.”

The pope is due to arrive in Bangui on Sunday. CAR has been volatile since early 2013, when Muslim rebels overthrew François Bozizé, who had been president for a decade. Unprecedented sectarian violence followed and has continued to erupt despite the presence of more than 11,000 peacekeepers and police.

Francis is expected to encourage an interfaith peace initiative involving the archbishop, the evangelical leader and Bangui’s imam.