The court held that high levels of benzoic acid and sunset additives in the popular soft drinks could pose a health risk to consumers when mixed with ascorbic acid, commonly known as vitamin C, according to local media.
Justice Adedayo Oyebanji ordered the Nigerian Bottling Company (NBC) to place written warnings on Fanta and Sprite bottles against drinking them with vitamin C, and awarded costs of two million naira ($6,350) against the National Agency
For Food and Drug Administration and Control (NAFDAC) for failing to ensure health standards.
"It is manifest that NAFDAC has been grossly irresponsible in its regulatory duties to the consumers of Fanta and Sprite manufactured by Nigeria Bottling Company," the judge said. "NAFDAC has failed the citizens of this great nation by its certification as satisfactory for human consumption products ... which become poisonous in the presence of ascorbic acid."
The incendiary judgment followed a lawsuit brought against regulator NAFDAC and the NBC -- a member of Coca-Cola Hellenic group which bottles Coca-Cola products in Nigeria -- by Lagos businessman Dr. Emmanuel Fijabi Adebo.
The claimant's company, Fijabi Adebo Holdings Limited, attempted to export Coca-Cola products to the United Kingdom for retail in February 2007.
But authorities in the UK seized and subsequently destroyed a shipment, Adebo claimed, because the products contained excessive levels of sunset yellow and benzoic acid. The latter substance can form the carcinogen benzene when combined with ascorbic acid, according to the US Food and Drug Administration (FDA).
Lawyers for the NBC argued that the products were not intended for export, but Justice Adedayo Oyebanji rejected this defense.
"Soft drinks manufactured by Nigeria Bottling Company ought to be fit for human consumption irrespective of color or creed," the judge said.
Mr Adebo was pleased by the verdict but vowed to pursue further damages.
"I'm happy that I'm victorious and we've alerted Nigerians and the entire world to what is happening in Nigeria," the businessman told CNN. "What the court fined NAFDAC is not one tenth of the amount I've spent on litigation ... We should have been awarded at least the amount that we spent in purchasing that product and in exporting it to UK. We are entitled to special damages for what we have gone through."
Both the NBC and NAFDAC are appealing against the ruling, arguing that the Coca-Cola products do not exceed benzoic acid limits for Nigeria or international limits set by Codex, the international food standards body administered by the Food and Agriculture Organization of the United Nations (FAO).
"The UK standards limit benzoic acid in soft drinks to a maximum of 150 mg/kg. Both Fanta and Sprite have benzoic levels of 200 mg/kg which is lower than the Nigerian regulatory limit of 250 mg/kg," wrote Sade Morgan, legal, public affairs and communications director of the NBC.
"The permissible ingredient levels set by countries for their food and beverage products are influenced by a number of factors such as climate, an example being the UK, a temperate region, requiring lower preservative levels unlike tropical countries."
Codex recently reduced its international limit for benzoic acid volume from 600 mg/kg to 250 mg/kg, and is considering a further reduction in the coming years.
"The previous levels are still considered as safe -- they are just not necessary," says Tom Heilandt, secretary of the Codex Alimentarius Commission, explaining the change. "More work will be done over the next few years to see if the levels could be further adjusted."
The levels found in Nigeria Coca-Cola products should not pose health risks, according to Dr Markus Lipp, a senior food safety officer at the FAO.
"The current acceptable limit for benzoates by the Codex Alimentarius Commission is set to be 250mg/kg," he told CNN. "This maximum use limit has a temporary designation, but nevertheless is considered for now to be appropriately health protective."
"There simply does not seem to be health concern from our perspective," Lipp said of the Lagos case.
Nigeria's health ministry also released a statement claiming that the products are safe.
"NAFDAC and SON (Standards Organization of Nigeria) regularly monitor the manufacturing practices of food industries and conduct laboratory analysis to ascertain continuous compliance with required national standards," said the statement.
However, Health Minister Isaac Adewole insisted that the government is responding to public concerns, and has opened an investigation into the safety of Coca-Cola products made in Nigeria.
Attempts to downplay the controversy are unlikely to succeed, at least in the short term, as alarm spreads among consumers.
Nigeria's Consumer Protection Council (CPC) has opened its own investigation.
"(The council) is extremely concerned about the questions that have arisen from, and on account of this judgement," said Director General, Mrs Dupe Atoki. "Fanta, Sprite and Coca Cola have arguably and consistently been the most widely consumed beverages in Nigeria. The spectrum of consumption is also perhaps the widest, with consumption starting as early as age four and far into adult years."
On social media, citizens expressed dissatisfaction with the way NAFDAC is handling consumer safety in the country. Several citizens accused the agency of placing more priority on generating revenues than protecting citizens.
With more citizens worried about their health following the revelation, some drew connections between NAFDAC's displeasing performance and Nigeria's worsening health statistics.
Since the verdict was made public, some citizens are choosing to stop drinking Coca-Cola products, with others calling for a boycott.
The NBC acknowledge they face an uphill struggle to contain the scandal and rebuild their reputation.
Coca-Cola hope that appeals against the ruling will be successful and rehabilitate the brands.
"The Ministry of Health communique could not be more clear that there is no issue with the safety of Fanta and Sprite," says Hamish Banks, Coca-Cola VP for Public Affairs and Communications, Eurasia and Africa. "The levels of all ingredients in these products, including benzoates and ascorbic acid (Vitamin C), are well within the conservative guidelines of the Codex Alimentarius and the Nigeria Industrial Standards."
"While it is not appropriate to comment further on a pending case and while the court considers appeals by NBC and NAFDAC against the ruling, it is evident that there is no safety issue associated with these ingredients," he added.
For one of the world's most successful and global brands, the hope is that the backlash does not travel beyond Nigeria's borders.