Shocking official figures reveal a surge in the incidence of bullying in the armed forces, with one in 10 military personnel claiming to have been the victim of "discrimination, harassment or bullying in a service environment" during the past year.

The figures, contained in the latest Armed Forces Continuous Attitude Survey, were described by defence minister Anna Soubry as serious, while a senior figure on the defence select committee said the bullying they revealed was very worrying.

The revelation came as a senior MP called for an urgent overhaul into the way the armed forces deal with sexual assaults and rape complaints. Madeleine Moon, a Labour MP and longstanding member of the defence select committee, said a new independent armed forces ombudsman was needed to properly investigate such complaints. Installing an ombudsman, Moon said, would allow service personnel to resolve grievances outside the chain of command and give them increased confidence to speak out.

The attitudes survey is the MoD's principal means of monitoring morale within the services. The number of complaints relating to discrimination, harassment or bullying in 2013 was up by two percentage points – a rise of a quarter – on 2012. Among junior ranks, those who said they had suffered abuse rose by four percentage points.

Overall, 8% of those who said they had been a victim of abuse felt so aggrieved that they submitted a formal written complaint, although it is not known how many related to alleged sexual offences as these are not categorised. The figures indicate that around 1,250 of the 12,500 service personnel who responded to the survey, of whom 3,446 were officers, suffered abuse in the military during the last year.

An MoD spokesperson said: "We recognise that it takes great courage for any individual to come forward and report a sexual offence and we have taken a number of steps to improve training and awareness to ensure that service personnel know how to report concerns and what support is available to them.

"The armed forces take this issue extremely seriously, which is why last year we set up a new database to improve the quality of information relating to service police investigations."

The MoD added that military police and the services prosecuting authority were independent of the military chain of command in the investigation of offences. They also said that service complaints were entirely separate from and outside the military justice system.

Meanwhile, Moon claimed yesterday that sexual harassment was a "daily issue" in the armed forces, and said she had been approached by numerous women who had made allegations of sexual offices in the army, only for investigations to be blocked by the military hierarchy. She told the Observer: "What we get is women saying, 'We don't trust the military justice system.' It's a very male environment, especially in the army – sometimes you have a single woman in a unit and it's very difficult for them to make a complaint.

"We do know that for some women the sexual assault or rape has taken place within the chain of command, but to make a complaint they have to go through that officer. They have been encouraged to drop the complaint or the complaint has been found to have no validity."

She said that she had tried and failed to obtain figures from the armed forces which would indicate the extent of the problem. Moon said: "They [the MoD] fail to take the issue seriously enough and are not rigorous in tackling and understanding the problem they have got."

This week, a new inquest will open into the death of Anne-Marie Ellement, a Royal Military Policewoman who hanged herself at Bulford in Wiltshire in October 2011 after she alleged she has been raped by two colleagues. An internal inquiry led to no charges being brought against the two soldiers.

The new inquest was opened after her family sought a judicial review into the handling of her case. They claim she was bullied and ostracised after reporting the rape. Her sister, Sharon Hardy, 44, said: "We want answers. She was such a strong girl, she had no fear, but they took all that away. They stripped her of her dignity."

A year ago defence ministers announced the creation of a special database to compile details of sexual offences relating to armed forces personnel. However, the figures are not being made public, and there remains no central record of the overall number of sexual offences involving the armed forces.

Lisa Langstaff of campaign group Women Against Rape accused the MoD of a "concerted cover-up" over the true extent of sexual offences committed by military personnel.

Shami Chakrabarti, director of Liberty, which has launched a campaign for military justice and is representing Anne-Marie Ellement at her inquest, said: "No wonder the defence establishment resists human rights applying to servicemen and women, when their rapes and sexual assaults go uninvestigated and unpunished.

"No institution can police itself, particularly when so used to quite literally 'closing ranks' in a crisis. The MoD needs to come clean about the number of young recruits who have reported rape by their comrades, and the urgent need for an independent armed services ombudsman is undeniable."