Ian Huntley felt 'hounded' by the police and press during the hunt for Holly Wells and Jessica Chapman, the Soham murder trial has heard.
The girls disappeared last year
His boss at Soham Village College said Mr Huntley, who denies murdering the girls, had talked about being depressed and wanting a break.
Margaret Bryden said the caretaker also told her he was the last person to see them alive.
Best friends Holly and Jessica, both aged 10, went missing on 4 August 2002.
They were found 13 days later in a ditch near RAF Lakenheath.
"I questioned him about how he could be the last person and he said "if only I had said something different (to them)," Mrs Bryden told the Old Bailey.
Mr Huntley's former girlfriend Maxine Carr, 26, denies attempting to pervert the course of justice and helping an offender.
Mrs Bryden told the court she had kept a diary during the search for the girls, and logged phone conversations between herself and Mr Huntley.
Margaret Bryden was "delighted" with Huntley as an interviewee
During the calls he told her his GP was treating him for depression and high blood pressure.
The jurors heard how Mr Huntley had beaten several other candidates to the post of site manager at the Soham College complex, which is on the same site as Holly and Jessica's school, St. Andrews Primary.
Mrs Bryden said she was delighted with the way he had fielded questions and she thought he was a "very level-headed person".
The college had adopted a cautious approach after the previous caretaker was dismissed for having an "inappropriate relationship with a 13-year-old pupil", she said.
Mr Huntley said if a girl became attracted to him he would report it to senior staff.
Mrs Bryden confirmed such an incident had happened and Mr Huntley had reported it.
The vice principal said Mr Huntley had found things difficult in the beginning and had problems managing his staff which often left him tearful.
Mrs Bryden also said that Huntley had "confided" in her about his father.
Cross-examining her, Maxine Carr's barrister Michael Hubbard QC said: "He made some pretty shocking and outrageous allegations about his father, did he not?
"He made some pretty shocking allegations about what had happened to him in
his early life.
"Did it ever occur to you that he lived in a world of his own fantasy?
"Did you ever think he was making things up?"
Mrs Bryden said: "There were times I thought he was exaggerating things but
did not think he was making them up."
Earlier, the court heard that Mr Huntley had spoken of a secret "quiet area" where he
went plane-spotting at Lakenheath - near the remote ditch where his alleged victims were found.
Mr Huntley talked of a place near the air base that he was not supposed to go to,
where "no-one ever goes", the court heard.
He told salesman Benjamin Hickling, who was also interested in planes, about
the spot when Mr Hickling visited the college in March last year, five months
before the girls died.
Witness Jonathan Watkins told the court he spoke to Mr Huntley at the sports centre in Soham on the night the girls went missing.
He asked Mr Huntley had he seen the girls to which he replied "no" and that he had "been away".
In the early hours of the following morning Mr Watkins was in the sports centre with police looking at CCTV footage when Mr Huntley returned.
Mr Watkins recalled: "I think he asked us, did we have any tape."
The case continues.