The C-130 aircraft left Pakse in southern Laos about 2pm local time with the three bodies and members of their families, and touched down at Wing 6 at Don Mueang airport shortly before 5pm Bangkok time.
The aircraft dropped off 10 navy divers and officials at U-tapao airbase in Rayong on the way from the Lao province of Champassak to Bangkok. It also brought home 13 officers of the Supreme Command and 10 police divers who helped in the search and recovery operation in Laos.
The bodies returned to Thailand were of Phakkawat Atriratnachai, Kanueng Chartkasamchai and Veekij Busarawuthanu. The body of another Thai victim has also been recovered and identified, bringing the number of the Thai victims found to four. He was Yanyong Apaanan, a PTT Plc engineer.
Yanyong's body is expected to return to Thailand on Wednesday.
A fifth Thai passenger reported to be aboard has still not been found.
Kanueng's body was being returned to his home district of Wiset Chai Chan in Ang Thong for funeral rites. The body of Phakkawat was sent on another flight to Hat Yai district, Songkhla, and the family of Veekij took his body to Kanchanaburi.
Lao Airlines reportedly agreed to pay US$5,000 (155,000 baht) to the relatives of each of the victims.
Kanueng's father Seng was at Don Mueang to receive his son's body. He said the financial compensation could not cover the loss to his family and he would fight for a higher payment.
"We wish he was still with us,'' Mr Seng said.
All 44 passengers and five crew died when Lao Airlines flight QV301 from Vientiane plunged to the ground and then into the Mekong River on Wednesday last week in harsh weather conditions as the pilots tried to land at Pakse airport. Part of the fuselage has been salvaged.
The signal from the aircraft's flight recorder, which could shed further light on the cause of the crash, was detected on Monday, but it has not yet been recovered.
Pol Gen Jarumporn Suramanee, an adviser to the National Police Office, who led the Thai team verifying the bodies, said only 42 victims had been recovered. A 43rd body was not included in the count because identification remained unclear.
As of Tuesday, the identities of 26 bodies had been verified. It is hoped the others could be identified in the next week, after DNA tests in Bangkok, he added.
Some Thais still remain in Pakse helping Lao authorities in the search and recovery operation.