The results of the Sunday elections, seen as the verdict on his three years in office, are expected to weaken his clout and might hamper his economic reforms.
The Kyodo news agency said Koizumi's Liberal Democratic party (LDP) was certain to miss its target of winning 51 of the 121 seats at stake in the election.
TV projections showed the LDP and the main opposition Democrats neck and neck at 46 seats each with about a dozen seats left to be decided.
But Koizumi's ruling coalition looked set to retain its majority in the upper house. It already holds a majority in the more powerful lower chamber, which chooses the prime minister.
LDP officials acknowledged that hitting their target would be hard, but Koizumi said that failing to do so would not affect his future.
"If the ruling parties can secure a majority, then it won't be a problem," the prime minister said when asked whether he should step down if his party missed the 51-seat target.
The exit polls showed the Democrats on track to outperform the long-ruling conservative party.
The Democrats had harshly criticised Koizumi's track record on reform as well as unpopular changes to the creaking state pension scheme and a controversial dispatch of troops to Iraq.
"If the ruling parties can secure a majority, then it won't be a problem"
prime minister, Japan
Analysts said a weak LDP showing would undermine the maverick Koizumi's influence inside his party, but that he was likely to stay on as long as the LDP won more than 44 seats.
"I think the Democrats will get more seats than the LDP. If so, Koizumi's influence will decline. But unless it is 46 or below, I think he will stay on," said Masayoshi Kuboya, a researcher at the Institute for Political Studies in Japan.
Koizumi, 62, came to power in 2001 on a groundswell of popular support for his promises to abandon the wasteful public spending that inflated Japan's government debt, and to privatise debt-laden public corporations and postal services.
Most economists say his record is patchy, and his support is only half of the 80% of three years ago when he led the LDP to a solid showing in the previous upper house election.
The upper chamber has 242 seats and half are contested every three years.