His remarks come days after his boss, Finance Minister Arun Jaitley rushed to clarify that the centre had no plans to tax farm income. It couldn't, he said, since the Constitution had authorised only state governments to tax agriculture.
The minister's adviser agreed. But he asked why none of the 29 state governments had done it. It was a rhetorical question. Mr Subramanian went on to give the answer: "Our political discourse doesn't allow us to do that".
But batting for introducing the tax, he did raise some questions.
Why is it so difficult to make the distinction between rich and poor farmers, he asked. The economist argued the government shouldn't concern itself what the source of income was and there was certainly no harm in taxing rich farmers too.
Mr Subramanian is the second economist in the government to make out a case for taxing agricultural income. The first was Niti Aayog member Bibek Debroy, whose remarks a few days ago have triggered the latest debate.
Mr Debroy had asserted that the "eventual answer" to expanding the tax base was "to also tax the rural sector including agricultural incomes above a certain threshold". This was the comment that Mr Jaitley was trying to distance himself from.
As expected, Virender Singh Mast, president of the BJP Kisan Morcha, opposed the suggestion. "I know that some people evade taxes by resorting to farming... small farming ... Go after them. But those who are pure agriculturalists... why this futile debate?" he said.