But the pod of around 60 mammals last night appeared to have left the shallow waters of Loch Carnan in South Uist, easing fears of a mass stranding.
The second whale discovered yesterday was found on an islet near the small island where a female was discovered on Saturday.
Conservationists said a post-mortem examination of the first dead whale showed it had died from an infection and not from head injuries.
Rescuers said the pod had spent the past four days at the sea loch and that the animals were following their instincts waiting for a sick mother to die.
The main pod, which was in danger of stranding, appeared to have left the sea loch but the hunt for them was halted yesterday because of gales and heavy rain.
Alisdair Jack, Scottish national organiser of the British Divers Marine Life Rescue, (BDMLR) said: "It is very disappointing to have found the second stranded whale – which was spotted at around 4pm.
"In a previous incident in October, over 30 whales were in Loch Carnan. When that other group of whales left they subsequently stranded in Ireland a few days later. Our fear has been that finding the first dead whale this time it would not be the last.
"We have suspended operations because of the weather. It has not been possible to reach the dead whale at the moment but we are hoping to assess the situation later.
"Some of our members have remained on Uist. Others have returned to the mainland, (but] some will stay on Skye for the time being in case they are needed."
The whales left the loch on Saturday only for them to head back a few hours later.
The first dead whale was found washed up on the island of Gasaigh – a tiny isle in the loch – the same day.
Dave Jarvis of BDMLR said: "It appears that what has been witnessed is a group of these extremely social creatures accompanying an ill individual and that the infection may have caused this animal to strand."
A preliminary examination of the first whale, carried out yesterday by Dr Andrew Brownlee, veterinary investigations officer at the Scottish Agricultural College, found "potential evidence of an infection" in the animal's melon – a large fatty organ found in the forehead.
Environment minister Stewart Stevenson MSP said: "The loss of life is very unfortunate, but a number of teams working together in South Uist has ensured that a greater tragedy has been averted.
"The MPV Hirta will continue to search for the pod and provide monitoring assistance."