E-InvoicingMalaysia

Best E-Invoicing Software for Logistics in Malaysia 2026: Full Comparison

Compare 21 vendors with LHDN-certified e-invoicing solutions built for Malaysian logistics businesses — pricing, Peppol, features and expert picks.

Updated 2026LHDN MyInvois CompliantPhase 4 Ready

Logistics and transportation businesses face some of the most complex e-invoicing scenarios in Malaysia. Transport invoices may involve multiple parties — the shipper, freight forwarder, customs agent, and end consignee — and a single shipment may generate multiple invoices at different stages. For cross-border freight, Peppol is especially important: the JB-Singapore and Penang-Haadyai corridors handle enormous volumes of cross-border trade, and Peppol enables seamless structured invoice exchange with partners in Singapore and other Peppol-connected countries.

Consignment notes, freight invoices, and port handling charges each have different tax treatments and documentation requirements. Logistics firms with government contracts (e.g., supplying to Petronas, government agencies, or public infrastructure projects) increasingly require B2G Peppol capability. Multi-party billing — where costs are split across multiple entities in a supply chain — requires software that supports complex billing workflows beyond standard single-buyer invoicing.

All E-Invoicing Vendors for Logistics (21)

Sorted by price, lowest first. Vendors marked Best Value are the cheapest option for this industry. Peppol-certified vendors are highlighted.

VendorPrice/moTypeLHDNPeppolAPISupport
Access UBSBest Value
RM 0On-premise✓———View →
Finexus AREMA
RM 0Standalone E-Invoicing✓Peppol ✓✓✓View →
InvoisPro
RM 0Standalone E-Invoicing✓Peppol ✓✓—View →
Million Accounting
RM 42On-premise✓——✓View →
QNE Accounting
RM 62SaaS✓Peppol ✓✓✓View →
Jom eInvoice
RM 79SaaS✓—✓✓View →
SQL Accounting
RM 80SaaS✓—✓✓View →
CelcomDigi Business
RM 88Standalone E-Invoicing✓——✓View →
Info-Tech
RM 90On-premise✓—✓✓View →
Odoo Malaysia
RM 100Hybrid✓Peppol ✓✓✓View →
Zoho Books
RM 100SaaS✓Peppol ✓✓✓View →
AutoCount
RM 120On-premise✓—✓✓View →
Wavelength
RM 150On-premise✓—✓✓View →
Deskera
RM 199SaaS✓Peppol ✓✓✓View →
Sage
RM 250Hybrid✓—✓✓View →
HashMicro
RM 350Hybrid✓Peppol ✓✓✓View →
Microsoft Dynamics 365
RM 700Hybrid✓Peppol ✓✓✓View →
SAP Business One
RM 1500Hybrid✓Peppol ✓✓✓View →
Oracle NetSuite
RM 2500Hybrid✓Peppol ✓✓✓View →
ClearTax Malaysia
ContactStandalone E-Invoicing✓—✓✓View →
Flick Network
ContactStandalone E-Invoicing✓Peppol ✓✓—View →

Top 3 Picks for Logistics

Expert-selected vendors based on fit, features, pricing, and adoption within Malaysian logistics businesses.

HashMicro

#1 Pick

Peppol-certified ERP with logistics modules, multi-party billing, and B2G capability for large operators.

From RM 350/moPeppol ✓LHDN ✓
View Details

Deskera

#2 Pick

Peppol-ready cloud platform suitable for mid-size logistics firms needing cross-border invoice exchange.

From RM 199/moPeppol ✓LHDN ✓
View Details

SQL Accounting

#3 Pick

Most common among Malaysian logistics SMEs with strong local support and MyInvois integration.

From RM 80/moLHDN ✓
View Details

Pricing Tiers for Logistics

Vendors supporting logistics grouped by monthly subscription cost.

Under RM100/mo

RM100–RM250/mo

RM250+/mo

* Prices shown are starting/from prices in RM per month. Actual costs depend on invoice volume, user count, and selected plan. Verify current pricing with each vendor.

Key Features for Logistics: Vendor Comparison

Industry-specific features across vendors that serve logistics businesses. Based on published vendor capabilities.

VendorPeppol Cross-borderFreight InvoiceConsignment NotesMulti-party BillingTransport Tax
Jom eInvoice–✓––✓
SQL Accounting–✓✓✓✓
CelcomDigi Business–✓––✓
Info-Tech–✓✓✓✓
Zoho Books✓✓–✓✓
AutoCount–✓✓✓✓
Wavelength–✓–✓✓
Deskera✓✓–✓✓
Sage–✓–✓✓
HashMicro✓✓✓✓✓

✓ = Feature supported based on published product information. Always verify with the vendor before purchasing. Feature support may vary by plan.

Frequently Asked Questions: E-Invoicing for Logistics in Malaysia

Common questions from Malaysian logistics businesses preparing for LHDN MyInvois compliance in 2026.

Why is Peppol especially important for Malaysian logistics companies?

Malaysia's logistics sector is deeply integrated with Singapore (JB corridor), Thailand (northern border), and regional ASEAN trade. Peppol enables structured invoice delivery to counterparts in Singapore, Australia, New Zealand, and EU countries without PDF emails or manual data re-entry. For the JB-Singapore corridor alone, Peppol can significantly reduce invoice processing time and errors.

How should freight invoices be structured for LHDN compliance?

Freight invoices should clearly identify the service type (transport, freight forwarding, warehousing, etc.), the MSIC code for the service, the shipper and consignee details, consignment reference, origin and destination, and any applicable SST. Service Tax at 6% applies to most domestic freight services. Cross-border freight may have different tax treatment.

How do logistics companies handle multi-party billing in e-invoicing?

Multi-party billing scenarios — where costs are shared between shipper, freight forwarder, and consignee — typically require separate invoices issued to each paying party. Your software should support issuing multiple invoices for a single shipment, each referencing a common shipment or job number. Avoid combining multiple buyers on a single invoice as LHDN requires one buyer per invoice.

Are consignment notes the same as e-invoices?

No. Consignment notes (or delivery orders) are operational documents confirming the movement of goods. E-invoices are financial documents submitted to LHDN for tax compliance. Both are required in logistics operations but serve different purposes. Your e-invoicing software should allow you to reference a consignment note number on the e-invoice for traceability.

More Logistics E-Invoicing Resources

Logistics Industry GuideFull e-invoicing guide for logistics businessesLogistics SaaS SolutionsCloud-based e-invoicing software for logisticsLogistics On-Premise OptionsSelf-hosted solutions for logistics businesses

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