'Sorrow will turn to hate'
Poles also organised protest campaigns on social media site Facebook, with a group called "No to the Kaczynskis burial in Wawel" attracting over 30,000 fans.
"If President Kaczynski had died of natural causes he would never have been buried in Wawel," Jerzy Meysztowicz, a Civic Platform (PO) politician in Krakow, told Reuters.
"All the president's faults will soon be in the spotlight and in many cases sorrow will turn to hate."
The leading Polish daily newspaper Gazeta Wyborcza also opposed the move, calling the decision "hasty and emotional" in a front page editorial.
But allies of the late president defended the decision, which was made after consultations on Tuesday between the church and family members, including Jaroslaw Kaczynski, the president's brother.
Wawel is a large complex of buildings on the Vistula river that includes a castle, cathedral and fortifications, and traces its roots as a centre of political power back to the end of the first millennium.
As well as Polish kings, the Wawel crypt also contains the bodies of legendary military commander Tadeusz Kosciuszko, who fought in the US war of independence, Poland's wartime leader Wladyslaw Sikorski, and national poet Adam Mickiewicz.
World leaders to attend
Sunday's funeral is expected to be attended by a number of world leaders, including Barack Obama, the US president, and Dmitry Medvedev, his Russian counterpart.
A total of 96 people died in the crash near Smolensk in western Russia on Saturday, including Polish military commanders, top opposition figures and the central bank governor.
Kaczynski and his entourage had been travelling to mark the 70th anniversary of the massacre of Polish officers by Soviet secret police near Smolensk when his plane went down in thick fog.
Elections to replace the president are expected to take place on June 20, but no formal announcement has been made.