A report from Footy Classified reporter Caroline Wilson from earlier this week suggested tensions had reportedly risen between the powerful Saints pair, causing disharmony at the top level at Linton Street.
When quizzed on the matter by media on Wednesday, Lyon said while his relationship with Lethlean was stable, but there may be some personnel concerned with recent changes at the club.
"I had the opportunity to voice (to Wilson) if there was any disharmony, and I certainly didn't do that," the St Kilda coach said.
"I know she spoke to Simon and he said that as well. So she'd take both of us at our word.
"Clearly when I've been transitioning into the club, there has been a new regime in football. Things are done differently and there are changes and teams are disbanded.
"There has been some change. I wouldn't say there is unhappiness but sometimes not everyone is comfortable with change.
"From my end and Simon's end we're fine. We have common friends and people professionally we have worked with.
"I haven't had one raised word with Simon since I have been here so that's the truth, or Simon with me to be truthful."
Following a strong start to the 2023 season, the Saints have lost four of their last five matches and are now susceptible to falling out of the top eight - sitting just four premiership points ahead of the 13th-placed Gold Coast Suns.
St Kilda will be looking to return to the winner's list for the first time since their Round 16 win over West Coast when they host a Brett Ratten-led North Melbourne outfit at Marvel Stadium on Sunday afternoon.
Lyon could be prepared to swing the selection axe following his honest assessment of the Saints' loss to the Suns last weekend, while pair Jack Higgins (knee) and Jack Billings (thumb) are anticipated to return from injury.
Luckless 2022 recruit Jack Hayes is in consideration to play his first game since injuring his ACL in April last year. The Woodville-West Torrens product has battled knee and foot injuries over the past 12 months and recently made his return through the VFL against Sandringham.
"We spoke to the players, we think there needs to be some changes," Lyon said.
"We've been quite stable but there's people that have played well and are in form that we'll bring in."
The Saints and Kangaroos will go head-to-head under the Marvel Stadium roof on Sunday at 4:40pm (AEST).