The Olympic champion, 29, was third overall at the end of a promising first day - traditionally her strongest - with a score of 3,928 points.
On Sunday she leapt a respectable 6.16m in the long jump but threw a disappointing 42.60m in the javelin.
With the 800m remaining, she has 5,544 points, still on course for the 6,200 needed to qualify for the Rio Olympics.
Ennis-Hill is competing in her first heptathlon since winning gold at London 2012.
A top-12 finish and score of 6,075 points would also secure qualification for this summer's World Championships.
Canada's Commonwealth champion and world silver medallist Brianne Theisen-Eaton leads ahead of the final event, remarkably achieving three personal bests on her way to a 5,834 score.
Follow latest updates and reports on the second day of the Gotzis Hypo-Meeting on the BBC Sport website on Sunday, 31 May.

Walmart will give JD.com ownership of Yihaodian's marketplace, including the brand, website and app.
In exchange Walmart will take a near 5% stake in JD.com, China's second largest e-commerce firm after Alibaba.
Walmart took full control of Yihaodian last year, but has struggled to grow its market share.
"We're excited about teaming up with such a strong leader in JD.com, and the potential that this new relationship creates for customers in China, as well as for our businesses," said Walmart chief executive Doug McMillon.
Walmart will be listed as a preferred seller on JD.com, offering it greater exposure to the Chinese market.
Walmart's Sam's Club brand will launch a shop on JD.com's website.
The deal will also help grow Yihaodian in the western and northern regions of the country where it is less well-known.
"We look forward to further developing Yihaodian, which has tremendous strength in important regions of eastern and southern China," said JD.com chief executive Richard Liu.
Yihaodian's sale of food and beverages, home goods and electronics accounts for just 1.5% of web sales in China, according to research firm iResearch
According to Walmart, the website had more than 100 million registered customers in July 2015.
The two companies also announced plans to improve supply chain management and increase the amount of imported goods.

"The gritters are now travelling to various workshops for maintenance, just like getting a car serviced," said a highways official.
The "low-risk" season begins in October with "high-risk" starting in November.
The county council said they had to think about the upcoming winter even when it was "boiling hot".
The fleet of more than 40 vehicles covers about 1,865 miles (3,000km) of roads including all major traffic routes and selected A and B roads.
Officials said the service was stood down in April but had to start again surprisingly soon.
Richard Fenwick, from county council highways, said: "The end of summer is a busy time, even when it is boiling hot we have to think about it.
"We have drivers go out during the day to make sure they know the routes, iron out any wrinkles."
The authority said it had about 35,000 tonnes of salt in stock and would expect to use about 25,000 tonnes in an average year.
Jessica Ennis-Hill has fallen from fourth to eighth place after six events at the Hypo-Meeting in Gotzis.
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Walmart has announced a partnership with the Chinese e-commerce firm JD.com to help revive the US company's struggling website Yihaodian.
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Gritting lorries and snowploughs have been out and about on Lincolnshire's roads - in preparation for the start of the snow risk season.