"....my profound apologies to everybody who feels hurt...," he said when asked by reporters to comment on the criticism by the industry for his terming the incident a 'warning' to managements not to 'push' the employees 'so hard'.
Fernandes was talking to reporters after attending a meeting called by External Affairs Minister Pranab Mukherjee to discuss the controversy created by his remarks.
The meeting was also attended by Home Minister Shivraj Patil and Defence Minister A K Antony.
His remarks evoked sharp reaction from captains of industry with Federation of Indian Chambers of Commerce and Industry president Rajeev Chandrasekhar describing them as shocking and Infosys chief executive officer Nandan Nilekani saying whatever the circumstances, murder cannot be condoned.
Seeking to end the controversy, Fernandes said he was sorry for his remarks.
"I would like to put an end to this chapter by saying I am sorry," he said.
Fernandes said class four employees were appointed on contract basis and many a times the contractors did not pay even minimum wages.
Claiming that his remarks were 'misunderstood', the labour minister said he was for the poor sections of the people and was raising their voice.
"If I have no right to speak, I will never speak," he said.
Fernandes had said 'simmering discontent' among workers might be the reason behind the killing of Graziano CEO L K Chaudhury at his Greater Noida office.
He had also said there were disparities in the wages of permanent employees and contract workers and felt that workers should not be pushed so hard that they resort to whatever has happened in Noida.