The rights watchdog said that analysis of the latest figures released by both companies established that Anglo-Dutch Shell reported 204 spills last year, while the Italian major ENI admitted 349.
"These figures are seriously alarming. ENI has clearly lost control over its operations in the Niger Delta," the southern, crude producing region, said Audrey Gaughran, Amnesty's Global Issues Director.
"And despite all its promises, Shell has made no progress on tackling oil spills," she added.
"In any other country," Nigeria's spill figures "would be a national emergency," Gaughran said. "In Nigeria it appears to be standard operating procedure for the oil industry."
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Amnesty also questioned the credibility of the figures provided by the companies concerning the total amount of oil spilled as a result of the 553 incidents.
The 30,000 barrels, or five million litres, reported is "highly likely to be a significant underestimate," the group said, citing poor reporting of spills in the Niger Delta.
The delta has been devastated by oil-related pollution for decades, creating resentment among a local population which has also largely missed out on the benefits of Nigeria's vast energy wealth because of corruption.
Amnesty has however challenged such claims, repeatedly calling on Shell and foreign companies to invest in needed infrastructure repairs.