ACM Angus Houston called the discovery in the southern Indian Ocean an “important and encouraging lead”.
He warned that the data were still unverified.
British naval ship HMS Echo is sailing to the area to investigate further.
It is expected to arrive in the early hours of Monday.
Australian aircraft were also on their way, ACM Angus Houston told reporters. Australian naval vessel Ocean Shield would be heading to the latest search area once it had investigated a third acoustic detection elsewhere.
Both HMS Echo and ADV Ocean Shield have technology able to detect underwater signals emitted by data recorders.
Malaysia Airlines flight MH370 disappeared on March 8 with 239 people on board. Investigators believe it crashed in the Indian Ocean although no confirmed debris has been found. The battery-powered signal from the “black box” recorders fades after 30 days.
After confirming details of the first pulse detected on Saturday which had “characteristics consistent with” an aircraft’s flight recorder, Angus Houston told a news briefing at Pearce Air Base near Perth of a second signal.
“[Saturday] afternoon Perth time, there was another acoustic detection less than 2 km [1.2 miles] from the original.”
The second signal lasted about 90 seconds, he said.
The search coordinator insisted the latest developments should be treated as unverified “until such time as we can provide an unequivocal determination”.
“We are working in a very big ocean and within a very large search area, and so far since the aircraft went missing we have had very few leads which allow us to narrow the search area,” he said.
“I assure you that we will follow up and exhaust every credible lead that we receive.”
A dozen military aircraft and 13 ships are already searching three areas about 1,240 miles north-west of the Australian city of Perth.
Australian PM Tony Abbott earlier said he was “hopeful but by no means certain” that the signal detected on Saturday was linked to missing flight MH370.
Haixun 01 picked up the first so-called “ping” signal at about 25 degrees south latitude and 101 degrees east longitude, state-run Xinhua news agency said.
The signal reportedly had a frequency of 37.5 kHz – the same as that emitted by the flight recorders.
Three people on board the boat were said to have heard the pings, which were not recorded as they came suddenly.
Xinhua also reported that a Chinese military plane had spotted a number of white floating objects about 60 miles away a few hours earlier.
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