Michael Gove was replying to David Simpson at a Westminster committee on Wednesday.
Mr Simpson said it was his view and that of several farm unions, that there was not enough emphasis on food production in the proposed legislation.
Mr Gove said the bulk of the bill was to do with farming.
However, he conceded that the first clause dealt extensively with a new payments system offering “public money for public goods”.
“I’m tempted to say Hamlet is all about Hamlet, but he’s not there in the first scene,” Mr Gove said.
Some industry groups have suggested that there is too much concentration on farmers being paid subsidy for providing environmental benefits such as water quality and biodiversity.
Mr Simpson said cynics might suggest the government was content for UK self-sufficiency in food to remain at around 60%, making space for cheap food imports in post-Brexit trade deals.
He said there was no encouragement in the bill for farmers and processors to invest in increased production.
Mr Gove said the government “absolutely” wanted to increase productivity and farm profitability in a way that was consistent with good environmental outcomes.
He used the example of Northern Ireland pig production.
Mr Gove said if new export markets could be secured in the Far East for cuts like trotters, that would drive the production of pig meat which could then be sold into the UK market, displacing imports of things like bacon.
Mr Simpson said it was important to “get the balance right” between food production and the environment and the bill should not be slanted “one way or the other”.
While the Agriculture Bill is predominately about England, a schedule in it does give officials in Northern Ireland some powers.
Farm minister George Eustice said departmental officials in Northern Ireland had told him that while it would not be appropriate to draw up a Northern Ireland specific farm policy in the absence of an executive minister, they did want to use the bill to take some powers.
He said these included the power to roll over the existing EU scheme and improve it by changing some of the “unnecessary administration”.
