BT and TalkTalk also singled out by watchdog.
According to the watchdog, the two companies generated the highest complaint volumes per 100,000 subscribers between October and December 2015.
Complaints against EE related to matters ranging from fault, service or provision issues, concerns with billing, pricing and charging and how it handled complaints.
In the case of Plusnet, fault, service or provision issues and complaints handling were the main drivers of complaints to Ofcom.
Figures also showed that BT and TalkTalk generated relatively high numbers of complaints throughout the final quarter of 2015.
Virgin Media and Sky, meanwhile, were the subject of the fewest complaints during this period.
Ofcom went on to note that the total volume of complaints against the wider telecoms sector was lower in Q4 than it had been in the previous three-month period.
However, broadband and fixed line services continued to generate the highest number of complaints during this time.