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Experts suspect the lights, which were also seen in other parts of the country, were probably meteors flaming out in the upper atmosphere.
Melissa Mebus of Houghton Bay was one of seven women exercising at a regular bootcamp on Houghton Valley School's playing fields around 6.30am when they spotted a strange object overhead.
Richard Hall of the Phoenix Astronomical Society suspects mysterious lights may have been part of a meteor shower.
"Someone said 'oh my good look at that' and we all were all sort of like 'what the heck is that?'"
"We had long enough to see it. It didn't just shoot past ... we had about five seconds which is quite a lot if you are looking at something," Mebus said.
She described it as long and black with only the two lights at either end visible against the dark sky.
"It wasn't a plane, that's for sure. I think it looked a bit like a rocket.
"We were all freaking out a little bit, it was that strange. It felt a bit alien-like."
"If they were meteors they would have been moving fast, they're not going to be an aircraft or anything like that."
Meteor showers were expected to hit the earth's atmosphere over the coming weeks and these sightings could be part of that phenomenon, Hall said.
"If you've got a shower coming in, you could have one meteor following the other one.
"These are often remnants of old comets that pass through and as the earth hits them all the meteors will appear to come from the same spot," Hall said.
The Wellington exercise group's observations were mirrored in other parts of the country.
On Weatherwatch website's meteor reports comments section observers spotted something similarly unusual at the same time.
Commenter Tim of Christchurch was cycling to work when he looked up and saw two lights at the same altitude, one following the other, moving very fast toward the west.
"I thought it was an early morning airliner coming in but there was no noise and they were travelling too fast. Time of observation was about 4-5 seconds. Seemed very low and unusual."
Graham in Hawera did not think it was a meteor. "It looked like a ballistic missile or a jet-plane's engine using its afterburner or a blown engine."
Annie Boanas of Island Bay was with the Houghton Bay exercise group.
At first glance she thought it was shooting star but its speed and the fact that there was more than one light made her doubt this conclusion.
"It was almost like a pole with a light attached at each end, but you couldn't really see what was between the two lights."
Navigation provider Airways spokeswoman Emma Lee said there were no reports of anything out of the ordinary flying at that location over Wellington at that time in the morning.
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