Gatlin, 35, who has served two doping bans, was booed before and after Saturday’s World Championship final at London Stadium, and when he was presented with his medal.
Lord Coe then said he would not “eulogise” about the American’s victory.
“I take offence to, with all respect, Lord Coe,” said Renaldo Nehemiah.
Gatlin, 35, clocked 9.92 seconds as he beat second-placed compatriot Christian Coleman and legendary Jamaican Usain Bolt, who was third.
Bolt, 30, was unable to secure a 20th global gold in his final individual 100m race before retiring.
Lord Coe told BBC Radio 5 live’s Sportsweek that Gatlin’s victory was “not the perfect script”.
He added: “I’m not eulogistic that someone who has served two bans has walked off with one of our glittering prizes.”
Nehemiah, a former world record holder in the 110m hurdles, told BBC’s Newsnight: “Lord Coe’s a part of the IAAF who set the rules, who set out the punishments, and when you serve the punishment you are supposed to be reinstated, which these athletes who have offended and abused some of these rules have, and if you don’t want them in you should change the rules.
“You don’t allow them in and then still condemn them.”
“I don’t condone doping but Justin Gatlin is not the poster child for it.
“He’s done his time, he plays by the rules, the IAAF reinstated him. They said if you come back we should accept that. So to put a narrative out that it’s just Justin Gatlin and he’s the bad guy, it’s really not fair. It’s inhumane. It’s unsportsmanlike.
“He won the bronze medal here in 2012 [Olympics] and no-one said a word. No-one said a word in 2013, 2014 or even in 2015. It was only when he started to challenge Bolt it became an issue.”
Nehemiah said that Bolt had “no problem” with Gatlin. “If it’s good for Bolt it should be good enough for everyone else. If the king, the legend is OK with it we should all be OK with it.”
Earlier the athlete’s father said the booing of his son was “disrespectful to the sport”.
Why was Gatlin banned?
In 2001, when he was still at college, Gatlin was given a two-year suspension for taking a banned amphetamine.
He successfully argued this was because of medication he took for attention deficit disorder and was allowed to return to competition after a year.
Then, in 2006 – having won the 100m and 200m double at the 2005 World Championships in Helsinki – he tested positive again, this time for testosterone.
Gatlin was banned for eight years, avoiding a lifetime ban in exchange for his co-operation with doping authorities. This suspension was halved to four years on appeal.
‘Boo the federations’
Toni Minichello, who coached Britain’s former Olympic heptathlon champion Jessica Ennis-Hill, earlier told BBC Sport fans were entitled to express their opinions by booing – but added the authorities also needed to be held to account.
“It’s not his [Gatlin’s] fault in any way shape or form,” he said. “It’s the fault of the federations and Wada [the World Anti-Doping Agency] for putting the rules down in such a way that allows him to return.
“Really, if you want to boo somebody, boo Wada, boo the federations.”
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