Two Hungarians and one Bolivian were killed in the shootout, said Hugo Escobar, the Bolivian police chief.
Morales, in Venezuela for talks with Hugo Chavez, the Venezuelan president, and Raul Castro, his Cuban counterpart, said he had ordered an operation to arrest the suspects.
"Yesterday I gave instruction to the vice-president to move to arrest these mercenaries and this morning I was informed of a half-hour shootout at a hotel in the city of Santa Cruz - three foreigners are dead and two arrested."
Morales also said an Irish citizen may have been among what he called foreign mercenaries involved in the alleged plot.
Alvaro Garcia, the Bolivian vice-president, later said the men were carrying guns and grenades and attacked police as they approached them.
'Weapons captured'
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| Bolivia was rocked by violent opposition protests against Morales' rule last year [AFP] |
Morales said that Garcia and a cabinet minister were also targets of the plot.
Mariana Sanchez, Al Jazeera's correspondent in Caracas, said: "We understand that President Morales had ordered their [the plotters] arrest in the [Bolivian] capital La Paz.
"So there may have been a follow up on this and it ended in a violent way.
"What we understand is that there was a shoot-out at four in the morning. Apparently, police raided the hotel where the men were staying.
"Police also captured explosives and a high-calibre weapon ... [and] a weapons cache."
Determined opposition
Morales has announced several similar plots against him in the past although the results of investigations have not been made public.
The Bolivian president, a socialist, is Bolivia's first indigenous president and has faced determined opposition from wealthy regions of the country, including Santa Cruz, over his plans to redistribute land to the poor.
Last year, opposition groups launched violent protests against a new constitution promoted by Morales that gives more power to indigenous Bolivians.
The Bolivian leader ended a five day hunger strike on Tuesday after politicians passed an electoral law creating more seats in indigenous areas where his support is strongest.