David Martin made his comments after The Herald revealed yesterday that young medics in a number of mainland Scottish health boards are routinely clocking up 87 hours per week despite an EU Working Time Directive - implemented in 2004 - that states staff should not be forced to work any more than 48 hours a week on average.
In Ayrshire, the maximum working week is 91 hours, comprising seven consecutive day shifts of 13 hours.
Mr Martin, one of the six MEPs representing Scotland in Brussels and Strasbourg said he read the article "with horror" and questioned why some Scottish hospitals were continuing to rely on such exhausting shift patterns in the wake of European laws intended to drive down working hours.
Doctors have complained the rotas are putting patient safety at risk.
Mr Martin said: "What is the point of me and my colleagues coming together with various experts in the field of working time and health and safety to draft legislation to protect the doctors and safeguard patients?
"What sense does it make for a health board such as Ayrshire to adopt rules that state staff should work no more than an average of 48 hours and then in practice have a '... maximum working week of 91 hours, comprising seven consecutive day shifts of 13 hours?'"
Meanwhile, David Chung, a consultant in emergency medicine at NHS Ayrshire and Arran, blames the problem on shortages of staff which he said were unlikely to be alleviated "any time soon".
He added that while there was a traditional bias in favour of large city hospitals receiving more trainees, the situation was now being exacerbated by an exodus of medics abroad to India, Australia and the Emirates, where doctors are better paid.
Mr Chung added: "Medicine is an international market, like banking. The contrast between the arguments to protect the "talent" in the City and an NHS short of doctors should be noted."