The cartoon showed a farmer with a cow knocking at the door of a room marked 'Elite Space Club' where two men sit reading a newspaper on India's feat.
On September 24, India made history by successfully placing its spacecraft in orbit around Mars, becoming the first country in the world to succeed in such anointer-planetary mission in the maiden attempt itself.
At just USD 74 million, the mission less than the estimated 100 million USD budget of the sci-fi blockbuster "Gravity".
Only the US, Russia and Europe have previously sent missions to Mars. Andrew Rosenthal, editorial page editor of the New York Times, wrote in a Facebook post that a "large number of readers" had complained about the cartoon.
"The intent of the cartoonist, Heng Kim Song, was to highlight how space exploration is no longer the exclusive domain of rich, Western countries," Rosenthal said.
"Mr Heng, who is based in Singapore, uses images and text - often in a provocative way - to make observations about international affairs. We apologise to readers who were offended by the choice of images in this cartoon."
Rosenthal said Heng "was in no way trying to impugn India, its government or its citizens". "We appreciate that readers have shared their feedback, which we welcome," he said.
After India's successful arrival at the Red Planet with the low-cost Mars Orbiter Mission (MOM), US space agency NASA has lauded it.
"It was an impressive engineering feat, and we welcome India to the family of nations studying another facet of the Red Planet. We look forward to MOM adding to the knowledge the international community is gathering with the other spacecraft at Mars," NASA Administrator Charles Bolden said.