Nigeria Customs Service spokesperson Joseph Attah said it was discovered in four containers of controlled and prohibited pharmaceuticals that arrived in Lagos from India.
The head of customs at the seaport, Jubrin Musa, said the drugs were not certified by the National Agency for Food and Drug Administration and Control as they exceeded required limits.
"Tramadol is not under trade prohibition but it is controlled and regulated," he told AFP.
"Where you import milligrammes over and above the control limit, that is where the law is infringed upon."
Boko Haram fighters are known to have used tramadol during their nearly nine-year quest to establish a hardline Islamic state in northeast Nigeria.
In December last year, the UN Office on Drugs and Crime also issued a warning about the non-medical use of the synthetic opioid across West Africa and its use by jihadists.
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It said the rise in consumption and trafficking of the drug was "serious, worrying and needs to be addressed as soon as possible".
Yearly seizures of tramadol in sub-Saharan Africa have risen from 300kg to more than three tonnes since 2013, according to the UNODC's World Drug Report 2017.
The report said the drug was mainly manufactured in South Asia and smuggled through the Gulf of Guinea by international criminal gangs into areas where Islamist extremists operate.
In September last year, more than three million tablets were discovered in Nigeria in boxes marked with the UN logo packed on a truck driving from Nigeria to northern Mali, it added.
Nigeria is currently battling a number of security challenges, including Boko Haram's insurgency.
Jubrin said the drug "could have further aggravated the already tense situation in the country" had it found its way into wider circulation.
One suspect has been arrested over the imports, he added.