Independent auditors are tussling with two major challenges during the coronavirus pandemic: conducting audits in a world gone remote. And doing so in a business environment beset with uncertainty.

Work-from-home mandates intended to stop the spread of the novel coronavirus are complicating auditors’ efforts to count inventory, assess changes in internal controls and track down evidence needed to sign off on companies’ financial statements, auditors say.

The disruption to business operations caused by the pandemic, meanwhile, is exposing companies’ liquidity problems and threatened debt covenants, which could result in auditors questioning going-concern assumptions. Companies are required to assess their ability to remain in business for the next 12 months. When an auditor doubts going-concern assumptions, the company’s relationships with lenders, vendors and customers can be fractured.

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Because of the pandemic, auditors have received some relief from regulatory inspections. And public companies have been given more time to file periodic reports. But auditing standards themselves haven’t changed, meaning auditors must embrace new measures to maintain audit quality.

“People might think that, in this environment, there’ll be some pressure to overlook some of those requirements or maybe accommodate a lesser quality of evidence,” said Jim Burton, partner-in-charge of audit methodology and standards at Grant Thornton LLP. “We’ve got no basis to do that.”

The challenges are likely to be illuminated in the coming weeks, as U.S. public companies prepare financial statements for the quarter ending March 31. Major concerns for many companies, however, may not come to light until the end of their fiscal years, when auditors provide opinions on the accuracy of financial statements.

Regulatory Relief for Public Companies and Their Auditors Public-company auditors have received relief from regulators as the novel coronavirus has disrupted business The Public Company Accounting Oversight Board, which regulates U.S. public-company audits, said it would give audit firms up to 45 days of relief from inspections amid the coronavirus pandemic. The move followed the Securities and Exchange Commission’s decision to give public companies an additional 45 days to file financial statements.

U.K. regulators said companies could delay the process of selecting new auditors and postpone rotating audit partners, which are supposed to change every five years. Audit firms and corporate-governance bodies have cited issues for companies and auditors in meeting reporting deadlines and completing site visits.

Auditors are monitoring issues companies are facing during the reporting season, such as difficulty performing valuation and goodwill impairment work given the market’s volatility, Tim Ryan, U.S. chairman and senior partner at PricewaterhouseCoopers LLP, said on a call this week with reporters. Auditors also expect companies to expand disclosures on potential future risks and uncertainties, he said.

With employees working remotely, many companies have changed which employees are responsible for certain internal controls or how a particular control is performed, said Phillip Austin, national assurance managing partner at BDO USA LLP. That introduces heightened risks that must be considered by auditors, he said.

A company performing cycle counts—a process for tracking inventory—several times a day may have to suspend that control, Mr. Austin said. In other cases, fewer or less-senior employees may be placed in charge of a control due to remote access. Finance employees may have to make additional reconciliations for accounts payable, payroll and bank transactions in changing those controls.

Being unable to visit sites to check inventory has emerged as one of the biggest obstacles for some auditors during the crisis. As a workaround, some companies are able to use earlier inventory counts to determine the year-end balance, defer accounts for later in the year, or use transactional records related to the inventory such as recent purchases and sales as alternative evidence, Mr. Austin said.

An auditor must review the available evidence and ask, ‘Does this evidence get us far enough?’, and in some cases it won’t, Mr. Austin said.

“Companies and auditors must simply adjust how we do what we do without compromising audit quality,” he said.

Auditors have long gained trust and confidence in their clients’ management abilities from observing them in the office. But that’s no longer an option in many cases.

If remote work continues for a lengthy period, that trust built over years of client-auditor relationships could be jeopardized, said John Chapman, vice president of finance at Kinder Morgan Inc., a Houston-based energy infrastructure company.

“It’s hard to not have that face-to-face meeting where you can get into the nuts and bolts of technical accounting issues,” Mr. Chapman said. “But we’ve learned to basically take advantage of these phone calls and conference calls if we need to.”

Related Video Stuck at home with a poor Wi-Fi signal? WSJ's Joanna Stern offers some fixes and advice on the best router to buy in her new work-from-home (aka WFH) tech-tip video series.

Write to Mark Maurer at mark.maurer@wsj.com