The EC made the move earlier on Thursday, filing a case against Poland, Hungary and the Czech Republic with the EU's top court for failing to comply with a decision to relocate refugees.
Asked by reporters to comment on this development, the foreign minister said "nothing has changed in this matter".
"Our position is clear - we disagree with the policy put forward by the EU two years ago", he added.
Waszczykowski's words were echoed by his deputy, Jan Dziedziczak, who said that when it came to relocation, the government was "carrying out the wishes of the Polish public, in line with the law and the European spirit", while the previous cabinet's contrasting ideas on the refugee problem "received a scathing assessment from the Polish people".
Meanwhile, Konrad Szymanski, a fellow deputy foreign minister - with a brief for European affairs - told PAP Poland was ready to make its case on the relocation of refugees before the Court of Justice of the EU.
Szymanski added the government would respond to the EC's move "in detail" after receiving the text of the submission to the EU's top court, which would probably arrive at the judicial body "in a few weeks".
Whatever happens, "nobody will relieve the Polish government of the duty to ensure public safety", the official emphasised.
Explaining its move in a statement, the EC earlier wrote:
"On 15 June 2017, the Commission launched infringement procedures against the Czech Republic, Hungary and Poland. The replies provided by the three Member States were not found satisfactory and the Commission decided to move to the next stage of the infringement procedure by sending reasoned opinions on 26 July 2017".
Although the Court of Justice of the EU confirmed "the validity of the relocation scheme in its ruling from 6 September", the EC noted, "the Czech Republic, Hungary and Poland remain in breach of their legal obligations".
"The replies received were again found not satisfactory", the Brussels officials emphasised, "and three countries have given no indication that they will contribute to the implementation of the relocation decision".
"This is why, the Commission has decided to move to the next stage of the infringement procedure and refer the three Member States to the Court of Justice of the EU", the EC stated.
The decision to relocate up to 120,000 refugees was made in September 2015 by the EU Council, featuring interior ministers of the member countries. The policy was adopted by a majority vote, with the Czech Republic, Slovakia, Romania and Hungary opposing quota-based relocation. Poland and Hungary refused to admit refugees under the scheme, while the Czech Republic only let in a small number. (PAP)
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