The Scottish Executive has said that sexual health is a priority on which £4.5m is being spent this year.
Rates of chlamydia are on the rise in Scotland
Health Minister Andy Kerr was responding to a survey of the UK's sexual health clinics by the BBC's Panorama programme.
It found that 45% of Scotland's 20 clinics could not treat a patient showing serious symptoms of a sexually transmitted disease within two days.
The 48-hour figure is not a Scottish target, but one set for England.
Mr Kerr said: "Improving Scotland's poor sexual health record is a priority for us. We want more people to take responsibility for their own sexual health and well-being.
"Our action plan, published earlier this year, sets out ways to deliver improved access to sexual health services in Scotland.
"NHS boards have been allocated specific funding totalling £4.5m this year to improve sexual health services in their areas.
"This will be directed towards improving clinical services and in particular, reducing waiting times and improving service access and availability."
Panorama contacted every clinic in the UK posing as patients and found that the longest wait for a routine appointment at any clinic was 30 days, while the average figure was 17 days.
Of those in Scotland which could offer a routine appointment when first contacted, none was available within 48 hours.
Some 20% could not see a patient whose partner had gonorrhoea within the recommended time.
Mr Kerr added: "Work on targets is being taken forward as part of the national Sexual Health Strategy.
"In addition, we have asked NHS boards to produce local clinical service plans to respond specifically to local needs."
Panorama's "Love Hurts" is broadcast on Sunday 16 October 2005 at 22:15BST on BBC One.
It is also available online at bbc.co.uk/panorama in broadband, live and on demand.