The team from Hawaii Pacific University says the false killer whale was seen struggling in the waters off South Point Friday.
The whale made it back out to sea at high tide, but ended up back on the Rocks Saturday.
"It's certainly a sad case because we know that there are so few of these Hawaiian false killer whales in the population. Knowing the animal was alive on Friday afternoon it really does tug at your heart strings," Hawaii Pacific University Marine Mammal Stranding Program head Dr. Kristi West said.
False killer whales are an endangered species to the islands with less than 200 of them left in the population.
"We have a situation here where the animal came in in a very remote location on the Big Island. It came in on a weekend and it also came in during a government shutdown. So this combination of factors has really forced us to take a look at how challenging this is going to be to keep moving forward in our current funding situation" Dr. West said.
On Sept.30, two-thirds of the grant money the mammal stranding program at HPU used to receive was cut.
This is the first stranding they responded to since that money was not received.
"We certainly miss the support of NOAA on the stranding response so this is a case where those are strong partners of ours and I certainly felt that we are trying to do a lot more with obviously a lot less," Dr. West said.
The HPU team says the whale weighs about 1,800 pounds and is more than 14 feet long.
Without the help of NOAA, Dr. West says they leaned on the community to figure out a way to get the carcass moved to a location where they could examine it.
"We have mobilized a team from HPU we worked with local community members in order to bring heavy equipment to the area that we could move the animal and examine it." Dr. West said.
Dr. West says she's thankful to the community in Ka'u who helped move the whale to a private landowner's property so a necropsy could be conducted.
She says it will be weeks before they know what caused the whale's death.
"We have looked at some of the organ systems. We did see some enlarged lymph nodes that may indicate the animal was struggling with some type of infection," Dr. West said.
Researchers are hoping to learn how the whale died to prevent other false killer whale deaths.
"We are trying to do things with less staff and less support, you know. We did have a team on the Big Island, but we could of used a team twice that size in order to do a really efficient job. So were are feeling the effects of the funding challenges we have," Dr. West said.
Dr. West is applying for more grant money to continue the whale stranding program.
The first runner to cross the finish line of the 2013 Honolulu Marathon was Gilbert Chepkwony who finished in 2:18:47.
A 3.8 magnitude earthquake happened just before 10:30 pm. Saturday at 6.1 miles east southeast of Holualoa on the Big Island according to the US Geological Society.
Thousands gathered at the memorial to pay tribute to those who paid the ultimate sacrifice and to those who survived.