The Daily Telegraph said it had secretly filmed doctors at a number of British abortion clinics.
The doctors are said to have agreed to terminate foetuses when women did not want their baby because of its gender.
Health Secretary Andrew Lansley said sex selection was "illegal and morally wrong" and he had ordered an inquiry.
"I'm extremely concerned to hear about these allegations. I've asked my officials to investigate this as a matter of urgency," he said.
The Department of Health also said it would be asking the General Medical Council to investigate individual clinicians and that the chief medical officer for England would be writing to all abortion clinics to "remind them of their responsibilities".
The Society for the Protection of Unborn Children (Spuc) said sex-selective abortion was an "inevitable consequence" of easy access to abortion.
In its report, the Telegraph said doctors had admitted they were prepared to falsify paperwork so the illegal procedures could go ahead.
The newspaper said undercover reporters had accompanied pregnant women to nine clinics in different parts of the country.
In three cases, the Telegraph reported, doctors were recorded offering to arrange terminations after being told the women did not want to continue with the pregnancy because of the gender of the unborn child.
Health Secretary Andrew Lansley vows that the claims will be investigated "urgently and thoroughly"
In a statement, Chelsea and Westminster Hospital NHS Foundation Trust said it "takes extremely seriously the allegations made against one of its consultants" and was "investigating these very serious allegations as a matter of urgency".
Another of the clinics named by the newspaper, Pall Mall Medical in Manchester, said it had "suspended clinical contact" with a doctor.
A spokesperson said: "The clinic does not condone in any way the referral for termination on the grounds of gender. Our policy makes that completely clear.
"As soon as this concern was brought to our attention the clinic took urgent action to stop any further appointments for terminations."
Spuc communications manager Anthony Ozimic said: "This investigation confirms the reality of eugenics in modern British medicine, in which some innocent human beings are deemed too inconvenient to be allowed to live.
"Sex-selective abortion is an inevitable consequence of easy access to abortion, a situation to which the pro-abortion lobby has no convincing answer.
"The government needs to cut its ties to private abortion providers and to abortion rights organisations, as they are complicit in sex-selective abortion domestically and internationally."
In England, Wales and Scotland, abortions are allowed before 24 weeks of pregnancy if it is believed that:
- Continuing with the pregnancy would be a greater risk to the woman's life or physical or mental health than ending the pregnancy
- Continuing with the pregnancy would be more of a risk to the physical or mental health of any of the woman's existing children
- There is a real risk the unborn child would have a serious physical or mental disability
- Two doctors have to agree to the abortion, or one in the case of an emergency.
Conditions are stricter for abortions carried out after 24 weeks. [almost sure above is a part of truth, before 12 weeks they are in a will, aren't they]In Northern Ireland, abortions are illegal unless the mother's life is at risk.
Dr Gillian Lockwood, the medical director of the Midland Fertility Clinic and a former vice-chairwoman of the Royal College of Obstetrics and Gynaecology's Ethics Committee, told the BBC the reports were "disturbing".
She said: "There have been reported cases where women have had a long run of boys or a long run of girls, or this peculiar new notion of 'family balancing' where couples decide they just want two children and the want one of each.
"A foetus being the wrong gender according to the prospective parents is not grounds for termination of pregnancy under any circumstances."
Dr Tony Falconer, president of the Royal College of Obstetrics and Gynaecology, said: "Anecdotally, there are social and cultural reasons for preferring one gender over another and we need to know more about why these occur.
"The issues are complex. For instance, women may be coerced or threatened with violence into having an abortion. The priority would be to identify who these women are and to provide them with support.
"Abortion is already heavily regulated in the UK and sex selection is only allowed in very specific conditions such as in the case of hereditary disease as stated in the HFEA Act 2001. Doctors must work within the law." ..
Source: BBC Online, 24 February 2012