The move was seen as an effort to dull criticism that the tax hike was an authoritarian move by the president.
The government had labelled Wednesday's rally a move "to defend democracy" and many in the crowd carried banners in the blue and white colours of the national flag.
However farmers have vowed to continue with their protests, saying any congressional vote would only be for a "yes" or "no" and would not modify the exisiting tax hike.
"We don't agree with the bill the way it was sent. We are asking that it be opened up so that lawmakers can agree on changes," Eduardo Buzzi, head of one of Argentina's four big farm groups, told Reuters news agency.
Kirchner raised export taxes in early March by presidential decree, triggering a three-month standoff that has seen farmers block highways and suspend grain exports.
The Argentine president says the tax hike will help redistribute farmers' profits for the benefit of poor Argentines.
But farming groups say the taxes will make it difficult for them to reinvest any profits to continue making a living.
Protests and road blockades have led to shortages of goods like meat, oil, flour, vegetables and fuel.
Al Jazeera's Latin American editor, Lucia Newman, says that while any congressional vote on the tax issue would be tight, the president's party has a majority in both chambers of congress and Kirchner has calculated that she will probably win.
Argentina is one of the world's biggest agricultural producers, accounting for three per cent of global farm exports.
But the protests have driven soy prices to near record highs and sparked concerns of political instability in Argentina.