The 39-year-old woman was giving evidence at the trial of Maclennan, 30, from Bath, England, who denies raping the boy at the Lochaber nursery between August 1, 2012, and May 23, 2013.
He is also accused of sexually abusing a three-year-old boy between March 2 and May 23, 2013, and a girl when she was aged between four and five between August 1, 2012 and May 23, 2013 at the nursery.
The mother told the High Court in Glasgow that her son was very upset on May 22, 2013, and added: “On May 23 he told me something while we were at home watching television.
“It was an alarming statement.”
Advocate depute Kath Harper said: “Was it about any person in particular,” and the mother replied: “Mark Maclennan.”
She was then asked what the nature of the remark was and said: “A sexual nature. I was making dinner and he just came out with it while he was watching television. I went over towards him and asked him to tell me again.”
The woman said that she then texted her husband.
When he arrived the boy was watching Fireman Sam on the television. The court heard that the couple contacted social services, who then contacted the police.
The three-year-old was interviewed twice by police.
Under cross-examination by defence QC Donald Findlay the mother denied a suggestion that her son could have seen her and her husband having oral sex or could have watched pornography.
The court heard that as a result of the boy’s remarks an investigation was launched and Maclennan was suspended from his job as nursery manager.
Two other mothers, whose children attended the nursery, told of receiving letters telling them an inquiry was underway, although they did not know any details or who had been suspended.
The mothers, both aged 34, told of speaking to their children after getting the letter.
One of the mothers said that she spoke to her daughter, who was five.
Ms Harper said: “Did she tell you something that concerned you,” and the mother replied: “Yes. I thought about it and decided to phone up the police.”
The other 34-year-old told the jury that she spoke to her son, who was three, the morning after receiving the letter.
She was asked what the child said and replied: “Well, basically that Mark was touching him.”
The mother added: “Right there and then I burst into tears and told my work I couldn’t come in. He never went back to the nursery.”
The woman said that she had spoken to Maclennan briefly when her son enrolled at the nursery and again when she was told her son had thrown a chair at a staff member.
She added: “Mark told me he had taken my son into his office for a time-out after that. He said he was worried about my son’s behaviour and was going to work closely with him.”
Earlier in the trial a university student claimed that Maclennan sexually abused her when she attended a drama club.
The woman, who is now 19, told the jury that she was groped and sexually abused when she was aged 12 to 15.
Maclennan denies sexually abusing her between October 1, 2007 and July 31, 2010, at Stirling and Dunfermline and of having indecent photographs of children in his possession.
The woman, who cannot be named for legal reasons, said she met Maclennan when she was doing amateur dramatics.
He was a volunteer and acted as a chaperone for children taking part in productions.
She told Ms Harper that the alleged abuse began when Maclennan was fitting her for a costume for a panto at the MacRobert Arts Centre in Stirling.
The woman said: “He said one of the measurements he needed was between my legs, for which he required me to remove my clothing. He asked me to remove my trousers and later my underwear as well. I found it odd.”
She said that the measuring tape was held against her legs and private parts and said: “I was very uncomfortable. I was frightened and embarrassed.”
The jury was told that on another occasion the girl took ill and was taken by Maclennan to the disabled toilets.
She said that he put an ice pack on her head and told her to lie down and then pulled down her trousers and underwear.
The woman continued: “He rubbed my stomach at first and then further down. He did this with both hands. I was slightly mortified.”
She told the jury that Maclennan also gave her lifts from her home to the amateur dramatics club in Stirling.
The woman claimed that on a number of occasions while her parents were not there, Maclennan sexually abused her.
She said on one occasion he pulled down her trousers and underwear and pulled up her top and groped her.
The court heard Maclennan also touched her inappropriately during a costume fitting for the pantomime Mother Goose.
The woman said: “He inserted his hands into the costume and touched my breasts.”
Under cross-examination by Mr Findlay, the woman was told: “Mr Maclennan denies anything inappropriate happened to you.”
The defence lawyer then asked her why, if what she claimed was true, she had not told her parents or the police.
She replied: “I was embarrassed and didn’t want to think about it. I didn’t know what to do.”
Maclennan denies all the charges against him.
The trial before Judge John Morris QC at the High Court in Glasgow continues.