Johnson was sent home in disgrace after metabolites of the anabolic steroid stanozolol were found in his urine sample following his victory over Carl Lewis in the 100m final in world record time.
Chondrokoukis' father and coach Kyriakos said the athlete would seek a retest after a positive test for stanozolol.
"I will fight - we will fight - to respond and see exactly what happened," a statement from Kryiakos Chondrokoukis said .
Johnson's fall from grace is still the biggest doping scandal in the history of the Games. After serving a two-year suspension he returned to competition but was banned for life after a positive test for excessive levels of the male sex hormone testosterone.
Hungarian discus thrower Zoltan Kovago, a silver medallist at the 2004 Athens Games, will also miss the Olympics after the Court of Arbitration for Sport said he had failed to provide a sample when requested. Kovago denied doping and said he had provided three samples within a four-day period around the time in question.
Another medallist from this year's world indoor championships, Moroccan 1500 metres silver medallist Mariem Alaoui, will miss the Games after a positive test for a banned diuretic.
On Wednesday the world athletics governing body also announced that nine track and field athletes had been banned for doping violations.
Also on Thursday, International Judo Federation president Marius Vizer announced that Saudi Arabia's female judo competitor will fight at the London Olympics without a hijab.
Wodjan Ali Seraj Abdulrahim Shaherkani, one of the first two female athletes sent to the Olympics by the conservative Muslim kingdom, will not be wearing the Islamic headscarf when competing in the women's heavyweight tournament next Friday.
Female participation in sports is a controversial issue in Saudi Arabia, where powerful clerics denounce women for exercising.
Usain Bolt, the sensation of the 2008 Games where he destroyed the 100 and 200 metres records, took pains to allay fears about his fitness and form at a news conference for the Jamaican team.
Bolt, who will carry the flag for the Caribbean island at Friday's opening ceremony, was beaten over both distances in the Jamaican trials by club mate Yohan Blake as he was clearly troubled by a tight right hamstring.
"It's always a wakeup call to be beaten in the season but it's better at the trials than at the Olympics," Bolt said. "It opened my eyes. I sit down and rethink a few things. But for me it's just about getting it right on the day. I'm all right.
"I'm thinking this could be one of the fastest 100 metres of all time... a lot of guys have been running fast because it's an Olympic year."
British Prime Minister David Cameron emphasised his government's commitment to ensuring a safe and secure Games.
More than 9000 extra police are walking the streets and 17,000 troops have been called in to cover a shortfall left by private security group G4S.
Security has been an overriding concern for the government and Games' organisers. The day after the British capital was awarded its third Olympics in 2005, four suicide bombers killed 52 commuters in London.
G4S caused a scandal by failing to meet its target for the number of guards it could provide, and on Tuesday said that it had deployed around 5,800 security personnel, still short of its revised objective of 7,000.
"This is the biggest security operation in our peacetime history, bar none, and we are leaving nothing to chance," Cameron told reporters at the Olympic Park.
"Obviously the biggest concern has always got to be a safe and secure Games. That matters more than anything else."
White House spokesman Jay Carney told a media briefing in Washington that President Barack Obama had "utmost confidence" in British security preparations for the Games.
Londoners took to the streets on another sun-drenched day to watch the penultimate day of the torch relay which passed some of the city's most famous landmarks on its way to Downing Street, official residence of the prime minister, and Buckingham Palace, the central London home of Britain's Queen Elizabeth.
"It's amazing, look, people are hanging out of the windows to watch," said 61-year-old sales assistant Ulla Davis. "The country has always been enthusiastic, it's just the newspapers that have been against it."
The feel-good factor was emphasised by London's tousle-haired mayor Boris Johnson in a speech to a rapturous reception at Hyde Park, venue of the triathlon.
"People are coming from around the world and they are seeing us and they're seeing the greatest city on earth," Johnson said.
"There are some people who are coming from around world who don't yet know about all the preparations we've done to get London ready in the last seven years.
"I hear there's a guy called Mitt Romney who wants to know whether we're ready. He wants to know whether we're ready. Are we ready? Are we ready? Yes, we are."
Romney, the U.S Republican presidential candidate, was forced to clarify a comment which appeared to criticise London's handling of the Games.
