"A limited number of executives/employees from Square Enix's headquarters in Japan will be attending E3 this year, given the recent worldwide spread of H1N1 flu," said the company in a statement.
Japanese developer and publisher Koei told Kotaku that it is only sending a small number of Japanese staff to E3, "due to the current nature of and concern over the influenza A (H1N1). As a result, there will be a limited number of staff from the company's Yokohama-based headquarters attending this year's show," added the company.
For our own part, we've had to cancel one E3 appointment so far due to these sudden restrictions. Hopefully that will be the first and last one, since--as in the case of Capcom--some developers aren't comfortable with their incomplete games being shown if they aren't there to personally oversee their demonstrations. This is going to be a packed, busy E3, and it would be disappointing if the games list gets shorter as we get closer to the show.