Co-chief scientist Professor Gerald Dickens, from Rice University in the United States, said significant new fossil discoveries were made that prove Zealandia was not always as deep beneath the waves as it is now.
More than 8000 specimens from several hundred fossil species were identified.
The discovery of microscopic shells of organisms that lived in warm shallow seas, and spores and pollen from land plants, revealed that the geography and climate of Zealandia was dramatically different in the past.
"The new discoveries reveal that the formation of the 'Pacific Ring of Fire' about 40 to 50 million years ago caused dramatic changes in ocean depth, volcanic activity, and buckled up the seabed of Zealandia," Dickens said.
Co-chief scientist Professor Rupert Sutherland, from the University of Victoria in Wellington, said it was previously thought that Zealandia was submerged when it separated from Australia and Antarctica about 80 million years ago.
"That is still probably true, but it is now clear that dramatic later events shaped the continent we explored on this voyage," Sutherland said.
"The discovery of big geographic changes across northern Zealandia, which is about the same size as India, has big implications for understanding big scientific questions, such as how did plants and animals disperse and evolve in the South Pacific?"
The discovery of past land and shallow seas now provides an explanation: there were pathways for animals and plants.
"Zealandia, a sunken continent long lost beneath the oceans, is giving up its 60-million-year-old secrets through scientific ocean drilling," said Jamie Allan, IODP programme director at the US National Science Foundation.
"This IODP expedition has offered insights into Earth's history, ranging from mountain-building in New Zealand, to the shifting movements of Earth's tectonic plates, to changes in ocean circulation and global climate."
Future study of the sediment cores will focus on understanding how Earth's tectonic plates move and how the climate system works. Records of Zealandia's climate history are expected to provide a sensitive test for computer models used to predict future climate change.
The Joides Resolution will conduct additional expeditions around New Zealand, Australia, and Antarctica over the next year.