SOURCE: BBC News (1-14-10)
Health minister Mike O'Brien made the apology in a statement to MPs - it comes after he unveiled a compensation package for survivors in December.
Pregnant women were prescribed the drug in the 1950s and 1960s as a treatment for morning sickness or insomnia.
It was withdrawn from sale in 1961 after babies were born with limb deformities and other damage.
Mr O'Brien said: "The government wishes to express its sincere regret and deep sympathy for the injury and suffering endured by all those affected.
# Developed in Germany in the 1950s
# Prescribed as a 'wonder drug' for insomnia, coughs, colds, morning sickness and headaches
# Link with birth defects shown in 1961 leading to the drug being taken off the market
# Affected babies commonly suffered missing or deformed limbs and severe shortening of arms or legs
# The drug also caused malformations of the eyes and ears, heart, genitals, kidneys and digestive tract
# Scientists believe the drug harmed the growth of new blood vessels in the developing embryo
"We acknowledge both the physical hardship and the emotional difficulties that have faced both the children affected and their families as a result of this drug, and the challenges that many continue to endure often on a daily basis."
His public statement follows the decision by the government to make more money available to the 466 thalidomide survivors in the UK.
The drug's UK manufacturer, Distillers Biochemicals, paid around £28m compensation in the 1970s following a legal battle by the families of those affected.
This has been subsequently topped up over the years by successor companies, although the average payout to the 466 survivors in the UK remains below £20,000 a year.
The government's £20m funding package is on top of this and will be shared out over the next three years.
It reflects the fact that survivors are living longer than expected and as a result will have increasing health needs.
The UK was the second biggest user of the drug after Germany. About 2,000 babies were born with problems linked to the drug with half of them dying within months of birth.
Another 5,000 were born elsewhere in the world.
Guy Tweedy, of the Thalidomide Trust, which distributes aid to survivors, described the apology as "absolutely wonderful".
"I'm highly delighted and so glad that it actually came, 50 years too late but never mind.
"It's an apology not just to thalidomide victims but to the parents who lost their children in the early days."
Mr Tweedy added the apology "means as much in some ways as the money".
Stephen O'Brien, the Conservative health spokesman, said: "I welcome the minister's remarks. Many thalidomiders have indeed waited a long time for this."