The watchdog growled the lack of concessions from Qualcomm means that there will be a lengthy investigation into the deal. Forms may have to be filled in, some of which will involve attachments.
Qualcomm, which supplies chips to Android smartphone makers and Apple had until 1 June to propose concessions to allay possible competition concerns over the biggest-ever deal in the semiconductor industry.
The EU competition authority's preliminary review of the deal ends on 9 June. It can either clear the deal unconditionally or open an investigation lasting up to four months.
During an investigation, Qualcomm could seek to convince regulators that the deal was not anti-competitive. Failing that, it might have to offer concessions.
Rivals had urged the European Commission to ensure they would still be able to use NXP technology known as Mifare once the deal is done, people familiar with the matter said.
The technology is embedded in access cards for buildings and public transport, as well as mobile phones which double as electronic wallets. Competitors also want Qualcomm to agree to fair licensing practices, the people said.