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However, the Foreign Ministry in Moscow now says that Russian and international agencies had monitored the ship throughout its strange three-week voyage.

Not correct, the Russians had no clue abut the position of the vessel, they were informed by NATO.:

Military intelligence from NATO helped Russia track down the Arctic Sea freighter which went missing for some three weeks, Russia’s ambassador to NATO Dmitri Rogozin said. The help was made possible via new NATO Secretary-General Anders Fogh Rasmussen after the two met in Brussels on August 11

Yevgeny Limarev, a former Russian security agent who is now a French-based consultant on Russian security affairs, said the Arctic Sea was likely at the center of a struggle between competing business and Kremlin clans in Moscow, and the Kremlin was forced to intervene to prevent an international scandal.
http://www.neurope.eu/articles/95600.php

The pirates didn't realize that the United States still has an ocean surveillance system, and NATO countries have substantial maritime surveillance capability. Apparently the Arctic Sea was found and tracked shortly after it was reported missing about a week ago. It took several days for a Russian warship to reach the scene, and make the arrests. Thus there was no publicity for the tracking effort until the Arctic Sea crew were safe.
http://www.strategypage.com/qnd/russia/articles/20090823.aspx

Crew members have told Russian news reporters that they have been told not to disclose “state secrets”, while well-informed Russian marine journalists have said they are now wary of commenting further on the case.
Even the suspects’ extensive tattoos - normally a reliable guide to identifying different sub-tribes of the Russian Mafia - have caused bafflement. “It is clear they are not our criminals, said Alexander Sidorov, the author of Russian Criminal Tattoos book, after examining TV footage.
http://www.telegraph.co.uk/news/worldnews/piracy/6074439/Pirate-in-Arctic-Sea-mystery-had-been-dead-for-three-years.html