By default EEE should be disabled, if not you can disable it using ethtool using the following commands:
To check the status of the intel nic:
ethtool --show-eee <INTERFACE_NAME>
To disable EEE on a NIC:
ethtool --set-eee <INTERFACE_NAME> eee off
EEE could also be disabled in the NICs settings using Intels Lanfonf tool.