"Kaita has so far received more than 1,000 threats to his email from within Nigeria," said team spokesman Peterside Idah.
"We are taking these threats very seriously. We've spoken to the Nigerian government to inform them about it and also written to FIFA to notify them," Idah told Reuters by phone from Nigeria's base some 200 km (125 miles) north of Durban.
Nigeria were leading 1-0 in last Thursday's game when Kaita kicked out at Greece's Vassillis Torosidis on the touchline in the 33rd minute. The referee showed him a straight red card.
The west African side went on to concede two goals, seriously damaging their chances of getting to the second round of the tournament in South Africa.
"We consider it a very serious matter because this is a young man who is putting his best at the service of his country and football," Idah said.
"That is why the team received the news of the threat to his life with shock and disappointment and is urging the authorities in Nigeria to take measures to protect him."
He said the 24-year-old midfielder was "terribly shaken, but, fortunately, he is receiving great support from his team mates and team officials".
Nigeria take on South Korea at the Moses Mabhida stadium in Durban on Tuesday and must win to stand any chance of qualifying.
The team spokesman said defenders Taye Taiwo and Elderson Echiejile, who suffered injuries in the match against Greece, were making "good recovery" and might be available for their final group game.
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