Ukraine fans hurled several lit flares onto the field soon after kickoff and also after Serhiy Nazarenko's 29th minute matchwinning goal which ended England's Group 6 winning run at eight games.
Football Association spokesman Adrian Bevington said on Sunday that the FA was deeply concerned about the incidents. He said referee Damir Skomina was twice forced to stop the match, on the first occasion for two minutes, while the flares were put out and removed.
"We have spoken with the FIFA delegate and we will be submitting a report with regard to the missiles," Bevington said. "We will be following that up with a formal complaint. It is not acceptable for any player to come under attack from sustained missile throwing and we will be forwarding that to FIFA next week."
The England players said, however, that the incident had nothing to do with England's first loss in the group after eight victories. Although England had already secured a place in the World Cup before Saturday's game in Dnipropetrovsk, the team wanted to go to South Africa on the back of 10 straight qualifying victories.
"What happened with the flares did not break our concentration at all," striker Wayne Rooney said. "It is a similar situation to when someone has gone down injured for a few minutes and play has to be stopped. You just get on with things."
Robert Green became the first England goalkeeper to be sent off, when he was shown a red card for bringing down Ukraine's Artem Milevskiy. That means he misses Wednesday's game against Belarus and England on Sunday called up Manchester United's Ben Foster to the squad as backup to David James.