The decline was in both wholesale and retail markets, with wholesale down 21.4 per cent, and retail down 15.2 per cent.
NZX noted that May's increases were on the back of a MSCI Standard Index rebalance, which saw Ryman Healthcare move out of the index.
June had seen an increase in value and volume trading in ETFs and debt.
Sarah Minhinnick, NZX's general manager capital markets origination, said the markets were reflecting world events.
"We are seeing more investors seeking security within debt and ETFs, given ongoing market volatility," she said.
"Clearly, the New Zealand market - like other markets globally - have been impacted due to that ongoing uncertainty.
"There are some quite big factors underlying that at play - inflation and rising interest rates - and you have got big geopolitical events happening as well.
"June's (NZX) result demonstrates that trading on equity markets remains soft but we are seeing increased activity in the debt markets and in ETFs, so there has been a re-evaluation as to where investment flows are going.
"We are clearly seeing that bonds are back," Minhinnick said.
June was a strong month for debt listings, with five total listings (BNZ, ASB, Infratil, and Vector), including one new green bond listing by Genesis.
Average NZX Debt Market (NZDX) yields were over 5 per cent, up from 1.75 per cent in June 2021, and there had been a continuous flow of new debt listings through the second quarter.
"Investors are allocating capital for those high yields and with ETFs as well," Minhinnick said.
Some investors were seeking security by diversifying across a range of securities through ETFs rather than investing in single stocks.
This week, ANZ became the first bank to announce its intention to access capital to help it meet new regulatory capital requirements and manage its capital position, lodging a product disclosure statement for an offer of up to $250m.
The bank is offering perpetual preference shares (PPS) - equity with bond-like characteristics - to retail and institutional investors.
Minhinnick expects to see more banks raise funds from the market.
The benchmark S&P/NZX50 share index remained impacted by macro-economic and geopolitical events caused by inflation, rising interest rates and the war in Ukraine.
Value traded on the NZDX in June was $228.3m, completing an almost linear increase in debt value traded during 2022.
This brought the total to 15 debt listings so far in 2022, adding about $3.4 billion to the debt market.
ETFs were also strong with value traded in June of $204.1m.
This represented the largest month this year with the exception of March.
