* PM and deputy have been in fractious coalition
* Military denied takeover bid, capital calm on Sunday
* Deputy called to talks in South Africa - minister (Adds deputy to hold talks in South Africa, AU reaction, background)
By Marafaela Mohloboli and John Mkhize
MASERU, Aug 31 (Reuters) - Lesotho's Deputy Prime Minister Mothetjoa Metsing has taken charge of the government after the Prime Minister Thomas Thabane fled the country accusing the army of staging a coup, a minister said on Sunday.
Thabane, who has been in a fractious coalition government with his political rival Metsing, left for neighbouring South Africa on Saturday after the army surrounded his residence and police stations in Lesotho's capital, Maseru, and gunshots rang out.
One policeman was shot dead and four others wounded during the confrontation, said police senior superintendent Mofokeng Kolo.
The army denied trying to force the prime minister out of power, saying it had moved against police officers suspected of planning to arm a political faction in the small southern African kingdom.
Diplomats in Maseru told Reuters on Saturday the army was largely seen as loyal to the deputy prime minister, while the police force largely supported the prime minister.
Regional power South Africa condemned the army's actions and later invited the deputy prime minister to talks there on Sunday, Lesotho's Minister of Communications, Science and Technology, Selibe Mochoboroane, told Reuters. He did not specify who the talks would be with.
"Constitutionally, in the absence of the prime minister, the deputy prime minister takes the reins," said Mochoboroane, who is also spokesman for Metsing's party.
"For now there hasn't been any arrangement, but it goes without saying the deputy prime minister will still oversee other issues that need to be taken care of until the prime minister returns," he added. On Saturday, Mochoboroane echoed the army's assurance that no coup had taken place.
Relations have been stormy between Thabane's All Basotho Convention party and Metsing's Lesotho Congress for Democracy (LCD) group, which formed a coalition with another party after elections in 2012.
Thabane dissolved parliament in June to avoid a no-confidence vote against him amid feuding among the ruling parties in the mountainous state of two million people, encircled by South Africa. Metsing later said he would form a new coalition that would oust Thabane.
The African Union said on Sunday it would not tolerate any illegal seizure of power.
Lesotho has undergone a number of military coups since independence from Britain in 1966. At least 58 locals and eight South African soldiers died during a political stand-off and subsequent fighting in 1998.
Besides textile exports and a slice of regional customs receipts, Lesotho's other big earner is hydropower exported to South Africa from the massive mountain ranges that have made it a favourite of trivia fans as "the world's highest country" - its lowest point is 1,380 metres (4,528 feet) above sea level. (Additional reporting by Aaron Maasho in Addis Ababa; Writing by Helen Nyambura; Editing by Andrew Heavens)