On this occasion, the church, in 's-Hertogenbosch, had already decided not to serve communion, so the protesters left, shouting and singing.
The dispute began earlier this month when a priest in a nearby town refused communion to an openly gay man.
The Netherlands was the first country to introduce gay marriage in 2001.
Most Dutch people support gay rights, but the Roman Catholic Church teaches that homosexual activity is sinful.
This dispute began during Dutch carnival celebrations earlier in February, when the man chosen to be carnival prince in nearby Reusel was refused communion because of his open homosexuality.
The refusal offended many in the local community.
The Sint-Jan church in the city of 's-Hertogenbosch, also known as Den Bosch, was prepared for the protest and so decided not to give out Holy Communion during Sunday Mass.
Several hundred demonstrators, dressed in pink wigs and clothes, left the church in protest.
The man at the centre of the row has said he just wants equal treatment - if he is regarded as a sinner, he wants the priest to refuse communion to all other sinners too.
BBC News
