After opposition leaders created uproar over the cartoon they said was insulting, Human Resource Development Minister Kapil Sibal said he was not personally responsible for the row but had "no hesitation in apologising to the nation".
He said a committee of the HRD ministry was already reviewing all such "objectionable matters in textbooks".
After Bahujan Samajwadi Party (BSP) chief and Dalit leader Mayawati wanted a time frame for action, Sibal said that Ambedkar was "not the property of any one segment".
"Ambedkar was a great man. I was not the minister at that time and not in the department. I took action the moment I got to know about it. The cartoon was objectionable and I apologise to the people that the cartoon featured in the book. We had no intention to condemn any section of the society," Sibal told reporters outside parliament.
"I have taken a further decision that the textbooks which contain this particular cartoon shall not be further distributed," he added.
According to Sibal, the issue came to his notice last month and he decided April 26 that the cartoon be withdrawn from the NCERT books on political science and the Indian constitution.
"Much before the issue came to parliament, I had already taken action. I called for the NCERT text books and I looked at other cartoons. I realised that there were many other cartoons that were not in good taste and disparaging in nature. They were not sending the right message to our children in classrooms," he added.
"All such content will be removed from NCERT text books next year. The cartoon was of course objectionable. This should be withdrawn," Sibal said.
The issue rocked both houses of parliament.
While the Lok Sabha was adjourned for the day at 2 p.m., the Rajya Sabha was repeatedly disrupted over the row.
After being adjourned thrice over the cartoon row, when the upper house met at 2.30 p.m., BSP chief Mayawati insisted that Sibal should clarify on the issue.
"Not only is the parliament but the whole country unhappy," she said demanding it be treated as a criminal offence.
Mayawati was joined by members from all parties including Lok Janshakti Party's Ramvilas Paswan, Rashtriya Janata Dal's Ramkripal Yadav, CPI's D. Raja, BJP's Thaawar Chand Gehlot and CPI-M's T.K. Rangarajan.
After Mayawati sought a time frame for action, Sibal stressed that Ambedkar was "not the property of any one segment".
Earlier, the Rajya Sabha was adjourned thrice and lost half of the question hour over the cartoon row.
The issue was raised halfway through the question hour by BSP member Brajesh Pathak, who said the government was being anti-Dalit.
As BSP members, joined by RJD members, walked towards the chairman's podium, the house was first adjourned for 15 minutes around 11.32 a.m., then for two minutes and finally till 2.30 p.m.
The controversial cartoon, first published in 1950s by cartoonist Shankar in his weekly magazine and reproduced in NCERT Class 11 political science textbooks, depicts former prime minister Jawaharlal Nehru with a whip in his hand chasing Ambedkar, who is seated on a snail, representing Constitution.
The cartoon depicts Nehru as asking Ambedkar to speed up the work on the Constitution.
The issue was raised by Dalit activist Thol Thirumavalavan, the Lok Sabha MP who heads the Viduthalai Chiruthaigal Katchi of Tamil Nadu, where protests were staged over the row.
Thirumavalavan, supported by members cutting across party lines, flashed a placard highlighting the issue and walked towards Speaker Meira Kumar's podium.
He said the cartoon was "insulting to Ambedkar, Nehru and the whole nation". At one point, an agitated Thirumavalavan even sought Sibal's resignation over the issue.
Leader of House Pranab Mukherjee said the printing of the cartoon in the textbook was "totally wrong" and that he "entirely" agreed with the sentiments of all sections of the house.