Kaczynski made the comments in an interview with the daily Dziennik newspaper which was published on Tuesday.
Asked by the newspaper if he would sign the treaty, the last step needed for full ratification in Poland, Kaczynski said: "This is now pointless. But it is difficult to say how this whole thing will end."
Kaczynski, a Eurosceptic often at loggerheads with the strongly pro-EU, centre-right government of Donald Tusk, Poland's prime minister, said it was wrong to suggest that the EU could not work without the new treaty.
"The bloc functioned, functions and will go on functioning. It's not perfect but such a complicated structure cannot be perfect," he said.
Shortly after the president's remarks, Tusk defended the treaty.
"We are convinced the treaty's ratification is in Poland's best interest ... It is hard to accept a situation where Poland would be put in the same position as Ireland, a very troublesome position," he said.
Kaczynski said that it was difficult to predict the end of the ratification crisis prompted by the Irish "No".
The president compared the bloc's current situation to 2005 when the French and Dutch voters rejected a more ambitious EU constitution, which was later reworked into the Lisbon Treaty.
The treaty also faces difficulties in the Czech Republic, which joined the EU with Poland in 2004.
The Czech Republic's highest court has been asked to rule on whether the treaty is in line with the constitution, delaying ratification until late 2008.
Kaczynski's comments came on the first day of the French presidency of the EU.
Nicolas Sarkozy, France's president, is due to go to Dublin on July 11 to try to address Irish voters' concerns there.
In Paris, a senior source in Sarkozy's office said France believed that Kaczynski and Vaclav Klaus, the Czech president, could be brought around to signing if they were told clearly there would be no further EU enlargement without the institutional reforms.
"For a country like Poland, the best argument is enlargement... It was a grave mistake to enlarge the EU in 2004 before reforming its institutions. That enlargement has gone well but we are not going to repeat that mistake," he said.