Pope Francis has received a rather unusual gift from Bolivia's first indigenous president Evo Morales during his visit to Latin America: a crucifix carved into a wooden hammer and sickle, the Communist symbol of the union of labour and peasants.

The 78-year-old pontiff drank the trimate – a tea of coca leaves, camomile and anise seeds – on the flight to Bolivia from Ecuador to alleviate altitude sickness. La Paz airport sits at 4,000m above sea level and for health reasons the Argentinian pope will be in the city for about four hours only. The pontiff lost part of one lung to disease when he was younger.

Pope Francis praised Bolivia for taking "important steps" in social security and to include the poor in the political and economic life of South American poorest country.

Morales, an anti-clerical champion of indigenous rights, has taken decisive steps to empower Bolivia's 36 native groups and embed their rights in the country's constitution. The president has also acted to change the constitution in 2009, making the Catholic nation a secular country and removed the bible and cross from the presidential palace when he took office in 2006.

Morales praised Francis as someone who is "helping in the liberation of our people". He gifted the pontiff with a cross with the Communist symbol similar to the one belonging to Father Luis Espinal, a Jesuit priest who was detained, tortured and killed by Bolivia's paramilitary squads.

"Remember one of our brothers, a victim of interests that didn't want him to fight for Bolivia's freedom," Francis, a Jesuit himself, said from the popemobile to a crowd. "Father Espinal preached the Gospel, the Gospel that bothered them, and because of this they got rid of him."

Francis and Morales met on several occasions, most recently in October when the indigenous president took part in a Vatican summit of grassroots groups of natives and advocates for the poor.