Former Southampton youth officer Bob Higgins left Saints in 1989 and joined the Malta FA until 1994.
Higgins is accused of historical sexual abuse against young players.
He has denied all allegations of wrongdoing and was acquitted of sexual abuse charges in 1992.
On Tuesday, former Southampton and England forward Matt le Tissier claimed he had been given a "naked massage" as a boy by Higgins.
Le Tissier, who joined the Saints aged 16 in 1985, said he was not abused but the incident was "very wrong".
On Wednesday, Malta FA president Norman Darmanin Demajo gave a news conference confirming Higgins had been suspended between 1990-92 when the original allegations were made, reinstated on a year's probation after being cleared, and then left in 1994.
The anonymous ex-Malta youth player told Malta's national Broadcaster TVM, working with BBC Sport, that he "never saw any abuse", but that Higgins used to drive him in his car and "put his hand back and touch my leg".
"It was very normal for Bob Higgins to get naked and have a shower with us," he added. "No-one was allowed to leave without having a shower, then he used to come in and a have shower with us."
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The BBC understands Higgins left Southampton after concerns were raised about his behaviour and a TV documentary then broadcast the testimony of eight alleged victims.
Southampton have said they are working with police and investigating how the club handled these issues in the past.
The BBC has made several attempts to speak to Higgins without success.
The FA has launched an internal review into historical abuse allegations throughout the game with more than 350 alleged victims having contacted police and 55 professional and amateur clubs connected to allegations.
A former Malta youth footballer has claimed a coach at the centre of sex abuse allegations would "shower naked" with young players during his five years working with the Malta FA.