John Swinney told MSPs a minority of pupils would not be able to take all the subjects they want, but he said this had likely always been the case.
He said since Scottish education was restructured to create the Curriculum for Excellence, pupils had been given a wider range of opportunities.
Conservative Liz Smith raised concerns over evidence the committee has heard on a narrowing of subject choices in S4.
More than half of the pupils who responded to a Holyrood survey said they were not able to take all of the subjects they wanted to at school.
She said young people had told MSPs they "cannot take the subjects they want to take and need to take" due to how the subjects are being offered in fourth year.
She said: "They feel they want to do them in S4 and some of their peers are getting more options than they are."
Mr Swinney said: "I quite understand that there will be young people who are unable to make all the choices that they would want to make.
"I would venture to suggest that's probably always been a factor in Scottish education. I don't think it's worse now."
He said it would apply to a small minority, adding: "That is an inevitability about subject choice in any education system and I cannot sit here as Education Secretary and say I can guarantee unfettered choice for every pupil in the country.
"I don't think there has been a narrowing of choice. I think there's been a broadening of opportunity for young people."
Ms Smith said: "There is more choice. The trouble is that choice is not necessarily in the core subjects in S4 for an awful lot of pupils."
Mr Gray said previously there were fewer options to choose from but more subjects could be taken.
He asked: "There's a difference in choice between what you can choose from and how much you can actually choose?"
Mr Swinney said he disagreed, saying the focus should not be on the achievement at the end of a single senior year, such as S4, but at the end of the three-year senior phase.
Questioned on an explosion in teachers dealing with different exam levels in the same class, he said he had seen "no evidence" this type of teaching is "inherently damaging".