In the 24th century aboard Galaxy-class and Intrepid-class starships, security alerts had at least five levels of application (also referred to as conditions), each one for different types of situations. On certain space stations, security alerts were distinguished by color. A security alert could be activated with no stated degree. The ship's Security Chief was responsible for initiating shipboard security alerts. (TNG: "All Good Things...")
Apparently, such a security alert level also included the arming of on-duty personnel with hand phasers at all times as evidenced during the episode. Given the severity of the actions during this alert, it may be the highest level of alert, at least aboard Voyager in 2377, and may have been related to a full alert Janeway called for in 2366.
Picard once again instituted a condition 3 security alert and told the computer to shut down all transporter systems and shuttlebays as Wesley Crusher eluded the crew while they were under the influence of the Ktarian game. (TNG: "The Game")
Picard's secondary order implies that a condition 3 security alert did not include taking the personnel movement systems offline.
In 2369, Picard ordered a level 2 security alert, after it was learned that a faction of the Borg had changed their entire existence and a new objective. They were no longer interested in acquiring cultures and technology. Armed guards were posted on every deck. (TNG: "Descent")
La Forge already called a level two security alert aboard the vessel before making his recommendation, so this would imply that level one was of greater intensity than the other levels. A full alert might have been the same as a level one alert.
ChiefMiles O'Brien was interrupted while attempting to call a security alert by an alien intruder in Transporter Room Three. Worf expanded the alert to all decks after the intruder left the transporter room. (TNG: "The Bonding")