Images published in the Daily Mirror appear to show the live animals strung up as targets moments before being shot during a course at Nato's training facilities in Jaegerspris, Denmark.
The pigs are shot by marksmen to replicate battlefield wounds so military medical staff including British Army doctors can train in emergency surgery.
The so-called Operation Danish Bacon has been described as "impossible to justify medically, ethically and educationally" by animal rights group People for the Ethical Treatment of Animals (Peta) said.
The MOD said it had not yet seen the pictures.
"Our military surgeons undertake vital training in Denmark where they learn specialist trauma treatment skills that save lives on the battlefield," a spokeswoman said.
"All animals used in medical training are anaesthetised before they are treated and by participating in the Danish led exercises twice a year rather than conducting our own, we minimise the overall number of animals used."
The MoD argued that although the practice would not be illegal in the UK, approval would have to be obtained on a case-by-case basis from the Home Office.
The Government suspended British participation in the surgical training exercises in the summer of 1998 after they were brought to the attention of ministers.
But the courses were re-instated after it was determined there was ''no equally effective alternative'' and that it was ''entirely appropriate and, indeed, necessary'' for military surgeons to carry out training on animals.
A Peta spokesman said: "Eighty per cent of Nato allies have already ended the cruel use of animals in archaic military medical training exercises.
"Instead of shooting, stabbing, and blowing up animals, military personnel in these nations are trained to treat traumatic injuries using life-like human-patient simulators, such as the state-of-the-art Caesar military simulator."