"We still love each other and our brotherhood remains," Sonthi said, adding he had had spoken to Thaksin twice on the phone in recent weeks.
Sonthi led the September 2006 bloodless coup against Thaksin, accusing him of corruption and abuse of power, as well as insulting the country's widely-revered king.
The general's comments came two days after Samak Sundaravej, head of the pro-Thaksin People Power Party (PPP), was formally named as Thailand's new prime minister.
The PPP won the largest number of seats in nationwide elections held last month and now heads a coalition with a two-thirds majority in the lower house.
Thaksin, who has lived in self-imposed exile in England since the coup, faces an array of corruption charges in Thai courts.
Earlier this month his wife, Pojaman Shinawatra, said the former prime minister planned to return to Thailand in May to defend himself.
Hundreds of millions of dollars of Thaksin family assets were frozen by the interim military-installed government following the coup.
Speaking to reporters, Sonthi said his telephone conversations with Thaksin were arranged by unspecified contacts who were concerned about the country's deep political divisions.
Sonthi's comments came after his return to Thailand from a visit to the Middle East.
The trip had sparked rumours that the now-retired general was seeking political asylum in another country amid speculation that the PPP's victory in the December elections could lead Thaksin loyalists to seek revenge against the coup leaders.
Sonthi retired as army chief in September 2007 to take a post as deputy prime minister in the outgoing military-installed government.
During the election campaign PPP leaders repeatedly said that if they were elected they would bring back Thaksin, seek revenge against the generals who were behind the coup and appoint Thaksin as an economic adviser to the government.